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

Hi,
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.