When you have a Command Block with NBT data and you copy that with Ctrl+Middle Click.
If you have another Command Block with different NBT data and you still hold the first Command Block and use Ctrl+Middle click, it will OVERRIDE the first command block, even if there's free space in the inventory
Linked issues
Comments 5
@@unknown because it's a duplicate of MC-74234, which is marked as fixed. It doesn't make sense to mark all duplicates as fixed.
Confirmed for 14w30b.