SD.Next is doing the weirdest things from time to time. The startup script performs various git pull
operations on every start so it autoupdates parts of itself, causing itself to break sometimes. Depending on your installed plugins it might execute code from the web.
It does not upgrade itself automatically though.
I recommend deactivating all autoupdate features and/or snapshotting your installation. (For example with an LVM thin volume mounted to its installation directory and snapshotting it before each start, this will also snapshot the python venv stuff).