Easy fix,

Pull your primer assembly off the machine.

Pull the prime tube, and rotary primer disc off the assembly.

Pull the primer punch housing off the machine.

Now, lets start from scratch,

Primer punch assembly.  If the punch is protruding above the housing top surface, you need to pull the primer punch assembly apart to clean the debris out of it that is not allowing the punch to drop all the way back down.
[youtube]https://youtu.be/Ufbuc6FBXFY[/youtube]

If the punch is recessed below the top of the housing, then get Dillon on the phone to send you are replacement punch assembly.
Bottom line it, the primer punch should be flush with the top of the housing!!!!


Next thread the primer punch into the sub plate and tighten it, and make sure that the top of the housing and face of the primer punch is flush with the sub plate surface. .001" to .003" (thickness of about a sheet of paper is fine), but the top of punch face and housing face should not be proud, or way low of the sub plate surface.
If you have problems here, then get Dillon on the phone, since you may need both a new primer punch assembly, as well as a new sub plate if you have peen the hell out of the sub plate bottom by over tightening the primer punch assembly.

Here, the top of primer punch and punch housing assembly top surface is way too low to the face of the sub plate and you can see how the primers are not only dropping down to the punch surface, but carving the surface of the sub assembly out as the primers not used are carrier to the ski ramp afterwards as well.



Onto the primer assembly.
Start with the primer tube, and check the bottom of it (brass section) to make sure that is clean/bur free, and not oblonged where the primer is going to drop out of the tube brass section.  Most of the time you can just clean up the ID of the brass section to fix any flaws, but something you may need a new tube if the ID is way gone instead.

Next, put the tube in the blast sheild and seat the tube all the way into the assembly channel, then look at the bottom of the primer assembly to make sure that the end of the tube brass section is flush with the bottom surface of the primer assembly face.  Again, .001" to .003" is not bad for the end of the tube being slightly higher than the assembly surface, but you don't want more than this (end of the tube flush with the surface of the primer assembly being ideal ).  Here, most of the time is just a peen edge on the brass section seating flange lip that is holding the tube up in the step channel that just needs to be resolve instead, but some time you have a miss match that needs to be resolved instead.

Before you install the primer carrier back in the carrier, take a look at the wave washer (5) for the carrier center pin.
This is the correct way that the wave washer should be sitting, and don't forget to lightly grease. Also double check the rotary primer disc channels to make sure that you don't have a bur on one of them cause a less then stellar drop out of the tube to the disc channel to cause a problem there.
[url]https://www.dillonprecision.com/docs/650_Pg_53.pdf[/img]

Regarding the plastic primer follower rod, put a 45ACP on the top button of it to add a touch more weight to the follower tube.

Next of the list, break out your sub plate alignment tool, and make sure that the sub plate is correctly indexed to the tool head.  I bring this up, since one of you tool heads may be off and needs to be replaced to match the rest of your sets.  Not only this, but double check the amount of tension you have on the case rims at primer via the tension tab, and make sure that if you are using crimped primer pockets, that the crimps have been swagged out with enough radus taper to the primer pocket that the primer can find and enter the case primer channel cleanly a well.
Note, reason that I really like the 1050, and keep the swager in play.  Hence some cases the primer pocket pocket entry radius sucks to begin with (too dam sharp entry walled or still has some remnants of primer staking), and when you start adding in rims that are not ideal sized as well (rim tension via the primer assembly tension tab not centering the case in the shell plate over the ram), the primer really has no chance in hell of entering the  case primer channel cleanly to start with isntead; even if the case primer pocket is sitting dead center over the primer punch with primer on top of it.

Some will say that they will not use such and such brass, but if you just run the brass through a swager to clean up and taper the entry taper into the  primer channel to correct the problem, it does solve a lot of the brass priming problems isntead.
[youtube]https://youtu.be/rxe8xt_u1NI[/youtube]





Lastly, make sure that you have the correct primer tube and the correct primer carrier in play for the primer sizes being used.  Way too may times, the problem is either a large primer tube, or large rotary primer disc (or both) being used for small primers that cause a problem isntead.



So to sum it up, we want the brass section of the primer tube to be clean so no primers can flip in there, dam near zero gap between the bottom of the tube and the rotary disc so the primers don't have a place to flip as they are dropping into the channels, the surface that the primers are riding along, flush all the way to the primer ram so the primers can not flip there, and as well as the primer tube clean with enough weight on the primer stack via the 45ACP case on the plastic follower rod to keep the from flipping in the tube stack.  From there, all you have left is to make sure that the sub plate and shell carrier is correctly indexed, as well as the cases primer pocket raduis correctly, so during the only last of time that the primer is not being captive (on the punch and into the primer pocket), it a clean shot up with nothing for the primer edge to catch to flip the primer.
Note, when you are adjusting the shell plate indexing, make sure that the indexing tab is indexing the shell carrier all the way to the next potions, and not just the indexing ball pulling the shell plate into the final position.  
I bring this up, since the first mod you do for 9mm is clip the indexing ball spring and install a mylar ball so the shell plate is not snapping the last of the way to spill powder, and if you don't have the shell indexing  set correctly, then the shell primer pocket is not going to be in the correct position to receive a primer to being with.

Sub plate indexing and primer assembly to primer punch a touch(primer assembly not indexed to  primer punch when the assembly was reseated and bolt tightened) , and the shell plate way the hell out of tune as well.
[img]http://i.imgur.com/XuO73uG.jpg[/img]

If you have any question, then post photo's of your parts/problems,  and I can walk you through the needed corrections.

You have to determine if the issue is OAL or case is oversized first.

Once you know, then you can correct the problem.

What bullet, hence it .356", or sized larger for say a PC/cast type bullet?
If 356, may be over taper crimping and this is causing problems.  If sized to .357~.358" then will explain why the cases are not seating all the way in the ammo gauge.
Also, are you sure that the bullets are seat starting square to the case.  Could be a problem with not enough uniform flaring of the case mouth to allow a clean/straight entry start, or even the wrong bullet seating stem being used for that bullet nose type.

As for die set up, tend to just run Hornday  custom dies (combo bullet seater and crimper only used to seat the bullet), Mr bullet type M powder expander (dillon powder through expander is easy to mod to this type), and then a Lee carbide FCD in the last station to bullet crimp.  Hence when the round hits the FCD, it not only resized on the way in, but on the way back out after the bullet has been crimped as well.

Lee carbide FCD, and keep in mind that in 9mm, it has a taper crimping sleeve and not the roll crimp sleeve shown below for the 357 round.

Call Dillon for that tool.

dp.

The alignment tool will get the sub plate indexed with the tool head correctly.

if the indexing is set correctly, will get the shell plate indexed with the sub plate correctly. Again, we do not want to make the index ball to pull the shell carrier all the way over the last of the way, its the indexing that should be adjusted correctly to push the shell carrier all the way to the next position perfectly instead.  If you need to check this, pull the indexer ball and spring, put the shell plate back on, and with light finger tension on the shell carrier, index the shell plate via the handle to confirm that the shell plate indexer has been adjusted correctly.

When you install the primer assembly to the sub plate, cam the handle all the way up and back to get the primer rod through the primer rotary disc with the shell plate remove, and tweak the primer assembly as you are tightening the two primer assembly bolt, to get the  channel in the rotary primer disc dead center on the primer punch.

If all is good, and you did the checks I mentioned above, then the primer is flipping as is clearing the rotary carrier channel, but before it seats into the hull channel.

It could be as simple as the primer assembly retainer tab lever not being adjusted correctly for the case rim in play to get the case primer pockets center of primer rod,  it could be a bur on the top of the primer punch that is not lifting the primer level, or as started, the cases need to be swaged to get a taper raduis into the primer pocket so the primers can enter the case primer pockets cleanly.  
The primer retainer tab is pretty easy to adjust, and with the case pushed to the lever to just rim touch it, should be able to look straight down the case primer flash hole to see the center of the primer punch.
On the primer punches, when I have the spring removed so I can clean it, will make sure that the edges of the primer rod face are not shape or bur'd, so if the primer does need to slightly shift of the primer punch to center in the case primer pocket, the primer can do so cleanly.  Hence will use some 4oo wet dry with the punch spinning in the housing to slightly break the edges of the primer punch face to every so slightly bevel them, and even polish the face as well of the punch to make sure it dead flat.

As for cases, if you do have a primer that is flipping instead of entering the primer pocket cleanly with all the above adjusted correctly, then when you pull the case out that the primer tried to flip on, determine if the case should have been swaged better or not.

One last thing, being take a good look at the channels in the rotary primer disc, and make sure that one of them does not have bur in it that is not allowing a primer to drop cleanly into the channel with it drops out of the tube, nor be cleanly lifted out of the channel via the primer punch.   Hence here, will take polishing compound on a felt tip Dremel tool to go to town polishing not only the radius entries into the channels both side to polish them, but the channels that the primer will be ridding in as well.

To add, make sure that the press is bolt down solid, on a solid bench.   If the press if flopping around as you are using it, this alone will induce a great deal of problem.

On a new machine, should not have any wear on the cam block, but on older machines where you do have wear to the cam block, some times building up back side of the cam block with foil tape helps to make sure that the cam block is pushing the cam lever all the way in to fully index the primer rotary disc before Dillion has a chance to send you a new replacement block.

Or could be that the primer indexer arm tab is not getting a good grip on the rotary disc to cam it to the next position.

Or could be a bur on the dead end of the primer indexer arm that is not allowing the arm tab to grab the disc cleanly to begin with.

Of could be that the primer rod is not dropping all the way back down into the housing to bind the disc instead.

Really, just leave the primer assembly primerless, the shell plate off, and lever the machine a few dozen time to make sure that the disc each stroke is fully advancing so the disc channel is dead center of the priming rod before it start to push through the disc channel.  This will check timing and the only thing that would be left, is if the tip of the primer rod is not dropping back down in the housing, which will bind the disc as the primer get stuck on the side of the rod instead.
Note, when the disc is bound, the wave washer for the arm has enough give that it will allow the arm to cant that time without breaking anything.