I've witnessed this - I was camping an exit and watching the map. I don't recall exactly, but either the crate icon changed to the 'green running man' then disappeared completely, or the crate icon just disappeared. I believe it was the former.
Understanding that this was not expected behavior, I approached the crate expecting that whoever had retrieved the crate had lost connection, but found the individual stuck inside the crate. I took them out and then took the crate.