Marking something done and immediately undoing it results in the item disappearing temporarily (until the page is reloaded).
Particularly this happens when you undo before the "done" animation is finished. Evidently the animation is not cancelled.
To trigger take any item and mark it done via Ctrl+Enter, then immediately undo via Ctrl+Z before the done animation is finished.
Edit: I just found this similarly happens when "mark as done" is immediately followed by "show done". The item that was recently marked as done disappears at the end of the animation but it should remain on screen since all done items are now being shown.
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