Version info:
Minecraft: 1.19.2 (Fabric)
Item Scroller: 1.19.2-0.17.1
Applied Energistics 2: 12.9.3

With AE2 and Item Scroller both installed, you can no longer shift-click items out of AE2's terminals into your inventory. Shift-clicking from your inventory into the terminal works fine, though.

I kinda thought there was a slot blacklist with AE2 slots on it, but I think it was probably left somewhere on the way since the old 1.12.2 Forge versions. I'll need to add it back at some point. For now you can toggle on/off all Item Scroller functionality as needed, by default with Ctrl + S inside any inventory GUI. While disabled, it should allow the AE2 slots to work as normal.