I was getting the same error. To fix it I uninstalled SET, removed the remaining SET directories, and then reinstalled SET. There is probably an easier way to fix it but this worked for me =D.
Running SET 0.5 Code Name:"Pink Pirate". Ran the update and I keep on getting this - svn: URL 'http://svn.thepentest.com/social_engineering_toolkit/src/web_clone/linux' of existing directory 'src/web_clone/linux' does not match expected URL 'http://svn.secmaniac.com/social_engineering_toolkit/src/web_clone/linux' The updating has finished, returning to main menu..
The enemy is no longer ignorance - It is vigilance
I was getting the same error. To fix it I uninstalled SET, removed the remaining SET directories, and then reinstalled SET. There is probably an easier way to fix it but this worked for me =D.