Sometimes when you place an item in a crate you create a ghost item, all you have to do is place the ghost item in your inventory, exit the crate, and then the ghost item will not disappear

Can confirm and reproduce

possibly a bug with Quark rather then with the modpack. Try to reproduce in a standalone Quark install

Confirmed bug with Quark, and also forewarned by the dev himself on the creation of the Crate. The bug has already been reported on Quark.