EDIT: Well, saw it too late that there exists an issue like this.. sorry
How to reproduce:
Place a Wopper above a Curcible Inserter from Sky Resources. The chest above of the Wopper won't "lose" any Items, but the Crucible Inserter fills the Crucible and the multiblock just works fine. No items will be consumed.

Using:
Modern Skyblock Modpack V1.9.1
forge 13.20.1.2393
Wopper 1.11.2-r3
Sky Resources 1.6.6