yes, fragments of cap will get in the nose of the hammer and over the opening of the nipple. A simple nipple pick will clean the nipple for you.. or an old guitar string works great. Usually ond of the higer ones. Just a piece of tape, put the string between tape and you have an instant nipple pick.

As for the caps not seating all the way. Some caps are different in dimension. What kind of cap are you shooting?

Nipples do not always seem to come in the same standard also. Get some emory cloth/paper and a start to buff the nipple with it. All you are doing is smoothing it out a little and taking ever so little off the nipple diameter. After a good polishing like that you will find the caps side on deeper and stay there. Don't push them down with the hammer. You would be surprised how little it takes to fire some of the caps out there.