Well, that's essentially what the title says.
I've tested it with both the abilities menu and the equipment one.
Open one of them, close it. Put an inventory window of some kind roughly on the same position of the screen (i tried with cupboard and crates). Move some item on the inventory. If you had opened and closed the abilities menu, when putting the item on the container, it will try to study it instead. Likewise, if the equipment window was opened and closed, it will instead try to equip that item.
Also, it works even when the container window isn't involved.
Open the equipment window, close it, try putting an equippable item where the window was. If you can equip it, the character will equip it.
Edit: same applies for the inventory window. Open it, close it. Open the equipment window, get some item from it, try putting it where the inventory window was. It will put it in the inventory instead of tossing it on the floor.
Right now i've been able to reproduce the bug only on character windows - inventory, equipment, abilities menu.
Edit2: in doing so, you can also end up taking items from the inventory if the slot clicked upon was already occupied.