I got feedback that there is something wrong with the crates that didn't disappear when destroyed. I jumped into the server and indeed. Also there is some weird teleporting issues like it was the case on the SAS servers before they restarted every 24. This seems to happen for windows dedicated, so if this server is running with windows, it might be the same issue.
About the crates, I suspect the /media folder not to be up to date with the 0.95 files. If server binaries are updated, it of course also requires the /media folder so be updated as well.