Sometimes a nipple will get peened from being hit by the hammer, and the cap won't go all the way down.

What brand of caps are you using? CCI are longer, and fit tighter for me than Remington.

CAP I.D. Height
Rem 10 0.166” 0.175”
Rem 11 0.166” 0.154”
CCI 10 0.161” 0.163”
CCI 11 0.166” 0.165”
RWS 1075 0.165” 0.16