I think I figured out what's going on, based on life experience.
All dry goods (grain, pasta, pellets, etc) potentially contain insect eggs (like weevils). If they sit long enough in the right conditions the eggs hatch, and voila, bugs in the food.
The bugs and eggs are SO small, you don't see them unless you look for them and sometimes you still don't see them. It's possible that there are eggs (or bugs) in the dust trapped in the nooks and crannies of the Feeder or cage. So if there's food around they'll get to it. So, it's not really a feed infestation issue, it's that the Feeder has the issue and they get what they want from there.
@tambayo Thank you for your response. I free feed my kits up to 12 weeks. I'm guessing you free feed yours something other than pellets.