Just some thoughts you can try if you already haven't. I have a similar issue with my S1050 where the swage backer rod hits the case mouth on my rifle cases, ever so slightly, and maybe 10% of the time, it dents the case mouth. Dillon suggested that I, and maybe you should too:
1) push down on the shell plate opposite the problem die. If it's springy, tighten the shell plate.
2) if you are using the aftermarket bearing, remove it, reassemble and try again.
3) remove the shell plate, set it on a flat surface, as it would be on the press, and see if it rocks at all. Not likely, but you could have a bent shell plate.
That's all I have. Best of luck!