Shiftclicking delete item in creative doesn't delete all items at times

This is quite a complicated bug, but if you load in a full saved hotbar, then pick a block with middle mouse button which isn't already in your hotbar, the item you are currently holding goes into your inventory. Then if you load in the hotbar again and shift click on delete item in the inventory it will not delete the item in your inventory. Like I said quite complicated but that is how I have been able to reproduce the bug.