The game will just randomly forget that you have certain items in your inventory and thus not remove them when shift-clicking the "destroy item" button. After selecting and deselecting those items in your inventory and trying again, it works.

I've had this happen to me on multiple occasions in the snapshots, but I've been having trouble remembering to get screenshots. Sorry.

I'm unsure as to how this happens. It seems to only occur after messing around with saved toolbars and the pick-block function.