This was brought up on The Utah Defensive Carry forum by one of their members.
After several people made some guesses the OP resolved it by phoning Federal and talking to one of their reps.
Here's what he posted:
So, I finally got around to calling Federal on this. I talked to Ryan, he knew immediately what I was calling about. His first question, are you carrying an m&p 40? I hadn't even gotten around to telling him the caliber I was having issues with yet (I don't think). Yep, that's what I'm carrying.
Turns out, it's actually being caused by the m&p 40 magazine. This magazine has a pinch point towards the top of the magazine, over time the cartridge rotates and indents into the case in the area of the pinch point. The place where you will ordinarily see it are on the second and third cartridge down in the magazine. I can confirm this is where I have often seen it happening, which has always confused me. He said this is something they have done extensive research and testing on since they were having ammunition sent back exhibiting the same issues.
He also told me that it's entirely safe to fire these cartridges, so long as nothing else was wrong with the cartridge (e.g. setback). This is something they have tested as well, after you fire it the case will expand to normal dimensions as you would expect.
Here is a photo of the magazine and cartridge together. You can see the indent where the pinch point is located on the magazine and that it lines up with the indent on the cartridge.
My 40 cal. is a CZ RAMI so I don't have this problem but I thought I'd pass this on.