It's probably that they're gaining levels, particularly if your ships are a decent match, i.e. good experience.
Elvis, that's something else-ships in orbit repair faster/more than ships not in orbit, but, as for population, the cap doesn't apply until after the growth/repair is done. So say you're at 7/8 hp, and you're in orbit, and you recover 3 hp. You don't cap at 8, you go to 10/8, and then stop repairing.