I have an FNP-40 and have not had that problem. I deliberately load my magazines to full capacity at the range and when I chamber the first round I top off the first mag to test the guns ability to feed with 14 in the mag. I'm over 1,000 rounds and the gun has fed FMJ and JHP without a problem.
Sounds like you have a 9mm if you're removing 2 or 3 and still have 13 or 14 in the mag. Can't comment on that, because I don't have a 9mm, just the .40.