If I have a hive with empty bottles in it and shift-click a stack (or more than enough to overflow the bottle slot) it put the extras into the output slots.
In most cases this isn't an issue, but I automatically process all items that are in the output slots and the extra bottles clog the system.

Preferred behavior: Bottle slot in hive fills to full and excess are left in inventory as partial stack.

Also, shift clicking a stack of treats into the incubator puts the excess in the output slot. Same issue.

I don't really want to look at that code again. Maybe some day

Ya, it's really just a polishing step. Very low priority, but I wanted to mention it anyway, because if I didn't, I would feel bad cursing under my breath every time it happened :) Great mod. Love your work.

hehe, there's definitely a bunch of polishing to do here and there