This happens with all weapons in the game, since the beta anyways.
It happens the most when you are behind cover and pop out and I suspect it has something to do with code-timing where sometimes the time it takes to pop out from cover is faster than the actual animation of the model, and thus, stops it from completing the animation & looking out of alignment.
To quickly fix this issue, you can either:
A - Shoot a Round and the sights will line up (gives away your position however)
B - Duck back down behind the cover and then pop back out (sometimes it fixes it, other times it will make it worse and other times it won't do anything)
C - Break off the cover you are on and then aim
D - Break off the cover you are on and then go back on the cover and try again.