Playing Sky Factory 3, so MC v. 1.10.2 and v. 0.11.0+47 of inventorysorter.

Bug happened when I had converted some loot bags from a higher tier to lower tier which results in stacks of lootbags of 4 - but once you remove them from that stack, they can't get restacked, so what happened was that maybe 10 stacks of 4 lootbags when auto-sorted just filled the inventory and erased some tools of mine and of course some of the remaining loot bags.

You can see it in this gif.

Sadly, the item forces a stack size of 1 and then violates its own rules by giving you 4. There's not much I can do except special case this, and every item that does this would need its own special casing. Just be aware this happens sometimes and have a chest handy.