I've been getting the following error message when sorting certain inventories:

java.lang.IllegalStateException: Unequal before and after item counts

This seems fairly minor and doesn't seem to break anything. Hasn't resulted in any crashes so far.

After some experimenting, it seems the issue is caused when multiple Apotheosis Gems are in the inventory being sorted.

Same here, I didn't notice it happening specifically on gems, but it happens for me as well.

The issue apparently happens with Apotheosis' Gems and Coral Tombstone's Scrolls.
It may be because these are unstackable items.

Some people also reported this issue to the Inventory Profiles mod Git where some logs can be found but no solution yet.