To reproduce: get a command block, place it down and click in it. Set the type to repeat and always active. For the command, type in "/clear @a" Items will still be in your inventory but they can not be placed, however if it is in the first slot, using select block replaces the item, and that item also stays in your inventory.

It seems as though the game sees that there is a block there, so using select block will put a new item in if a different block is selected, however now you have two items in your inventory that are actually not there. Upon trying to place these blocks, they appear for a single tick and disappear, still in the inventory.

Deleting the command block (by breaking it) does stop the clear command, however the items are still in the inventory and act as I explained above.