I’m not a real sysadmin so take it with a grain of salt, but in all reality this is probably why you would choose something like Debian for a server instead a bleeding-edge distro. Debian quickly backports security updates and fixes but otherwise keeps everything else stable and extremely well-tested, which pretty much 100% prevents serious bugs from reaching its Stable branch. You may still need to figure out an appropriate strategy for keeping your Mastodon container updated, but at least the rest of your system isn’t at risk of causing catastrophic errors like this. Also, Debian Stable does allow you to auto-upgrade security patches only, if you still want that functionality.