This happens in vehicles, barrels, sea chests, and wooden crates. You'll have items in any container and when you are tying to pull out items certain ones (no pattern with it) will not leave the container. You can not move it directly into your inventory or to your hands then to inventory. I've tried logging out of the server and then back in. The only way I've been able to undo it is by asking the server admin (for a private server) to do a reset. This clears it up but only for a bit. I have confirmed that this happens on public official and private servers. The inventory management issues all around along with items becoming frozen in place need to be a primary item to fix as it affects all gameplay.