I have the same problem when shutting down the server from the terminal with CTRL+C (sending SIGINT). So for the sake of it I took another approach and did the whole process by joining the currently running server and shut it down logged in as an admin with the MP server command #shutdown.
I just recently made a fresh install of the Arch Linux OS and before that I was running an older kernel and possibly older Steamcmd version (sadly there's not a chance I would remember what they were) all the way to the beginning of December 2016. With the older build(s) I had sporadic Segmentation faults (around 1 out of 10 shutdowns, probably less) but now with the fresh-out-of-the-box install Segmentation fault happens with every shutdown.