There are a large variety of variables that can result in misaligned sights on an AR, making diagnosis and detection a difficult process.

EDITED TO ADD: Pictures
Please note: These pictures are do not represent defective or misaligned product, they are just meant to be helpful illustrations of the specific parts of the rifle.

The front sights are mounted working off aligning the index pin that is installed into the barrel extension. This index pin will represent the Top Dead Center (TDC). The center threaded bore of the front sight base (where the front sight post is installed), is lined up with the index pin to properly install the front sight base. Provided the bore is perfectly straight and the threads for the barrel extension are perfectly square, you will have a perfectly lined up barrel assembly.



Here is where it can get messy:
Looking at a upper receiver, if the index slot for the index pin is not machined perfectly on the center to hold the index pin at center, your front sight will be canted to one side.




For a flat top upper receiver, if the 1913-Pic rails that will hold your iron sight (at the position your iron sight is mounted) are not lined up parallel to a perfectly aligned index slot your front and rear sight alignment can appear canted.

Because rail mounted iron sights actually index off the right side of the flat top 1913-Pic rail, if that side of the rail is machined to thick or thin or the geometry is off, that will result in misalignment of the sights.




If the hole drilled to hold the rear sight aperture assembly (on a A2 or various BUISs) is not drilled on perfect center, that will result in misalignment of the sights.



If the hole in the rear sight aperture itself is not machined on perfect center, that will result in misalignment of sights.



So there are really a lot of variables to look at. Some will affect the sights more than others and some are easier to identify and isolate.

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With the m16 or ar15 you have a battle sight zero and then a true zero. with the m16 the trajectory of the bullet is the same at 36 yards and 300 yards. With this you can set your sights to your true zero. you have a elevation adjustment on your front sight and a left and right "windage adjustment" on the rear sights. as you sight in your weapon adjust your front sight for up and down and rear sight for left and right by using the knob on the right. don't worry about the tick marks on the back of the rear sight until you are done sighting in your weapon. afterward use it for windage. With the windage knob you can get your battle sight zero which is what your weapon zeros at taking wind and distance into account.

Hope this helps. My recruits usually took an entire week to understand this concept.

If theres any paly at all I always shim it and im always able to zero in 3 to 5 clicks.

Does anyone have a link for a how to do the "Pepsi can shim" for me? I have a BCM upper flat top and a FN manufactured barrel assembly. There is just a bit of play from left to right when inserting the barrel extension/index pin inside the receiver slot. Under torque, for tightening the barrel nut I can easily see the barrel rotating toward the right, giving a slight cant, when looking from the bore to the receiver. When I hold the barrel at it's left most position inside the receiver slot wall, again looking from the bore toward the receiver, then hand tighten the barrel nut, the FSB is then aligned perfectly. I need to make sure the index pin and barrel assembly cannot rotate to the far right wall slot under torque. Thanks for the help!