If you have already a Repetier-Server installation and you update using autoupdate or installing the new version manually, it can happen that the update fails.
One reason can be that the server was running a slow operation like rendering and the waiting for the process to finish timed out. In this case just wait for the process to finish or kill the Repetier-Server pocess and run the manual install again. Now it can overwrite the files and start the new version.