@PonyPC it could be any of your plugins.
In my case bedwars plugin was malicious, if you don't have any, just check out this thing, it might help you:
Just tried some quick edits by editing the server config then service pufferd restart
stopCode 2 doesn't work, but 9 and 15 do.
So I have gone with stopCode 15
Due to the process is given time to gracefully shutdown.