I finally figured out why my pip farms always become so overpopulated, and it's face-palm obvious.

I can't believe I didn't realize it immediately but I just figured out that it's caused by the cuddle pips. Their hugs make the eggs hatch faster, increasing the breeding rate significantly.

Once your first cuddle pip hatches, you have to watch closely or automate your population control, otherwise within 2 or 3 generations you'll have 50 pips starving each other out.