This is my 2nd rifle caliber suppressor. Had no issues with the first one, which was a .308 can. I previously shot the .308 can on my 5.56 SBR with no problems.

This one is a 5.56 can, and for some reason it's stringing shots to the left, if I take the can off, the rifle shoots fine. I used almost the exact same layout with this can as I did the .308, the only difference being 1 extra freeze plug in the 5.56, and a smaller blast chamber due to that.

Any input?

Did you check it with an alignment rod?

What does the shift measure, at what distance?
If you're not seeing any baffle or endcap strikes your alignment should be fine.
Do you have any shims?
If you did, you can index the can differently and see if the shift follows.
Its a thread together can? If so, have you tried aligning the baffle clips differently? Which way are they now?

Alignment is fine, no baffle strikes.

I do not have any of my baffles clipped.

It is a thread together can, I trimmed by blast chamber spacer to just the right length for it to thread together and have everything tight.

I can't think of anything that would be making it string shots like it is.

ETA: I was shooting at 25 yards, shot 3-5 inches to the left of where I was aiming, 6 shots made about a 4 inch line of holes.

How big are the holes in your baffles & endcap? 

What clips are you using on your baffles, if any?

What size is the tube?  What spacing on the stack?

9/32 holes

Full stack with a 1.25 ish blast chamber. No spacers between freeze plugs.

No clips on the baffles

7.6 titanium tube, 1.5 diameter. It's an sdtac d cell tube

Wouldn't hurt to make the holes bigger.
I used N size (.302) and 5/16 on the last few baffles and endcap.

My suggestion would be to over bore the baffles as he said but clip as well. May be cause by turbulence with tight bore and all.

I am going to open up my bore some as suggested. I'll try that and then move on to clipping baffles if that doesn't fix the issue. Will probably be Wednesday or the weekend before I can go shoot it again.

All of my 22cal (5.56 included) cans are drilled 17/64. Smaller than your 9/32 and none have had a destabilization effect.
I'm not saying that a tighter bore couldn't cause destabilization, but to assume that this would cause all shots to go to the left doesn't make sense.
If the tight bore is influencing bullet flight, the results would not show in just one direction, you'd have flyers everywhere.
This is why I suggest you try to index the can differently, to see if the bullet strikes track with the rotation.
Don't jump to start drilling out your bore, as it might not solve the issue and can decrease efficiency of the suppressor.

Even tinfoil can be a spacer, as you're only talking a couple thou.
The skin of a beer/soda can is about .005. If you can make 2 spacers with this, to shim the shouldering point between the can's mount and muzzle threads, you'll rotate the suppressor almost 105*.
Try this and see if your POI shifts to between 1&2 o'clock.

Clipping your baffles is recommended, but I'd solve one thing at a time.
Were your baffles drilled on a lathe or drill press?
I ask because even a center marked hole can result in a slightly non-concentric drill, once the item is moved between fixtures.

I'm worried about shimming it leading to it being off center and causing a baffle strike.

I drilled it out using a vise and a hand drill to 1/4 inch hole, then assembled the can, ran a really long 1/4 inch drill bit through the assembled can, then took it all back apart and stepped stepped it up to the 9/32. I did 3 other suppressors this way with no issues.

The shim wont move it off center. It will make it so that the can is not threaded down at the exact same point. it's just timing the suppressor differently. It will likely tell you what is wrong.

How would I go about making a shim for a externally threaded flash hider out of a coke can?

Does your FH have a square shoulder or taper mount?
If square shoulder, make the shim ID so it will slip over threads and the OD just larger than the shoulder OD.
If taper mount, you'll have to remove the FH and shim, as described above, between it and the barrel shoulder.

Nothing needs to be CalTech accurate. Just make sure the shim material is flat and nicely sandwiched between the mating points.

If its a SD build the QD mounts in general aren't aligned perfectly, also the pilot holes in end caps were not drilled centered on some.  Other than that inconsistancy in bore can cause this, if your plugs are formed with a jig this is less likely, but the holes could still be off, they could pressed into the tubes so the holes are not all perfectly centered.  Over-boring would help if this is the case.

On closer inspection of the baffles, there are 3 that have the faintest appearance of having been struck by a bullet. I've drilled those out the next size up. I'm going to try and go shoot it tomorrow and see how it does now.