I encounter what youre describing from time to time, and it seems for a couple of different reasons.
Mostly, its when Im in a hurry, I seem to have the issue more. A lot of times if you dont get the bullet indexed properly in the case mouth, you will get a bulge when you seat it, especially if youre working the handle hard.
Most of my pistol brass is a mix of head stamps. Brass often seems to differ a good bit from maker to maker, and when you flare the case mouths, you dont always get consistency in the flare. Inconsistency here, just aggravates the above.
If you dont get the case fully in the shell holder, the expander will often bulge the case on one side too. Using a taper crimp usually nullifies things here though, or at least reduces them.
I seem to have the issue more with with certain calibers when using jacketed bullets than I do with lead. I see this the most when I load jacketed bullets in 357MAG. What I have found here is, if I work the handle "slowly", it happens a lot less, if at all. If I work the handle quickly, its pretty much a guarantee Ill get a number.