I'm not 100% how this is even happening, but I thoroughly tested and Tough As Nails is definitely the culprit here:

It causes dragon eggs from the Ice and Fire mod to duplicate upon trying to break/pick them up. The dragon eggs are technically entities, if this means anything. I assume TaN could be causing this bug for other mods that use the same method that Ice n Fire does.

The Ice n Fire mod I'm talking about can be found here: https://minecraft.curseforge.com/projects/ice-and-fire-dragons-in-a-whole-new-light