Its been a while since I loaded ammo for my 45 ACP and I acquired a bunch of once fired brass from my cousin who instructs handgun classes. After depriming, tumbling and flaring out the case mouths, I filled my hand primer up with large pistol primers and WTH??? They wouldn't go in. I started looking at the cases and sure enough out of the 400 or 500 cases I had, I only had about 50 that took the large pistol primer. The rest of the cases were made for a small pistol primer. Now I have to be sure to predominately mark the ammo boxes as large and small so I don't have to go through that sorting process again.
So if you didn't know this, beware there are .45 ACP cases with both large and small primer pockets.

Went thru the same thing. Got some Federals for christmas presents. When I went to reload them, well, same problem you had. They seem to shoot alright with small pistol primers though. Just a pain in the butt to keep them all sorted out.