Have done some more testing and find some small things that I think should be considered to be fixed.
When making a new domain in EHCP it makes a new folder with different folders inside, among which httpdocs is. For installing applications the files goes into this folder. Sometimes it is needed to remove the whole application and install it again. If the domain is removed the created folder is not completely removed, and creates problems when setting up the domain again. i have solved it with rm - folder in linux shell.