[Baertram]

Testing it at the moment and using the keybind for deconstruction + settings for using non-unique itemIds is not breaking anything for me.

Will test the unique IDs now.
Edit:
Somehow I cannot rebuild this bug with only FCOItemSaver enabled. Did you try it with ONLY this addon enabled? There must be some other addon in combination which interferes then.

Tested:
-Mark/demark with deconstruction keybind
-Open container (marked/unmarked with FCOIS marker icon)
-Open container protected with FCOIS anti-auto loot + auto loot + take all in eso settings enabled
-Loot items from container
-Hover mouse over items in container
-Take out items from container
-Tested with 4 containes in a row to see if after looting/mouse hovering something changes
-Tested with uniqueIDs and non-unique IDs

Everything works like intended for me. I'm not sure what to do even more sorry.
Please disable ALL other addons excep FCOIS and check if the error still applies. If so please send me your SavedVariables file FCOItemSaver.lua which you should find somewhere ar c:\users\username\documents\Elder Scrolls Online\live\SavedVariables

I'll try to to rebuild it then with your savedvars.

If the error is gone then please check which other addons were enabled before and find out which one got to do with looting, changing autoloot settings, tooltips and/or containers.

Many thanks