Errors that can commonly occur are conflicts with customized files. By default, the hotfix does not overwrite modified files (unless you enable the Overwrite all files option in advanced mode):
For each conflict with a customized file, the process creates the new version of the file with the .new extension. You need to manually transfer your customizations to the new files and then replace the original ones.
Customized files that would have otherwise been deleted remain in the file system, with an added .deleted extension.
The modified file could have been modified by some antivirus, etc. If you are 100% sure oyu hav enot modified any files, let the hotfix tool overwrite them.