Raspberrypi running on ubuntu mate with some sever errors

[Seadragon91]

@Tmp How do you start the server? This looks like the server is not executed in his working directory.
Example:
I am in directory /home/user/ and the server is in /home/user/Server/Cuberite. Starting it then with ~/Server/Cuberite
Then the server can not find all the files and folders.

Also it would log many red lines in console:
Error (2) opening directory "Plugins/"
Cannot read data from file Prefabs/Villages/PlainsVillage.cubeset
and more