Ah, so the bumps were there before you painted over them.
H'mmm.
My wife and I faced this problem when we were painting our boat. The deck had probably 6 coats of paint on them, some better than others. As a result, large chunks were peeling off.
We chipped and sanded and tried to fair off the 'craters', but eventually, we bit the bullet and sanded down to bare wood, or nearly so.
I can't seem to post a clickable link, but there are some pics on my blog, unlikelyboatbuilder.com. I'll post them if I can, later.
I think it was worth the effort, and it was probably less total work than trying to 'fair' with paint.
Helps to have a helper, though!
-- John