When a Player clicks on a Item in a chest it is added to the lets call it cursor slot.
If it gets cleared while it is in that cursor slot it should disapear like it gets cleared from any other slot but it stays and gets crazy:

• If it is a Block, it can't be placed anymore
• It stays in Inventory until it gets deleted(creative)
• It cant be dropped anymore(q does nothing)

Here is a Video because it is difficult to show this bug in images:
https://www.dropbox.com/s/zxjsxd0v2g8tdx3/Video%20%2810%29.mp4?dl=0

It worked in 1.8 (other versions except 1.13 snapshot not tested)