Steps to reproduce :

1/ Put a chest in front of a stick piston, hook up the sticky piston to a pulse extender.

2/ Activate the pulse extender and try to put an item in the chest when the piston retracts.

3/ With good timing, the item will be removed from your inventory but not put in the chest.

I believe this also happens when you try to put an item in the chest when the piston extends.

It's easier to reproduce if there is a lot of lag going on, so it's very easy to reproduce on realms.