Rights problem at installatioin, delete cache, and some strange things over night

how did you do the update? It sounds like the user used for the update is neither www-data nor in the group of www-data.

Did you use a plain Ubuntu Image? Setting up a web server is not a plain vanilla linux server. I recommend using a management panel like Plesk or cpanel, which typically sets up linux in correct way to use it as a webserver.