I can confirm this one. Mining the inserter puts the item being held into your inventory but having robots deconstruct it causes the item to disappear from the game. I think the best way to fix it would be to disable the inserter (to prevent the inserter from grabbing another item which then has to be removed) and have one bot take the item and another take the inserter itself. This behavior would be like what currently happens when you order a chest deconstructed.