The main reason to see such error message is, some erroneous entries in the patch metadata files for files itself.
This might happen if you try to forcefully stop the server as soon as you start the server
When the server start up, it copies the patch files. If the server is forcefully stopped at that time using [ctrl+c], patching processes get immediately stopped and patch meta-data will get corrupted.
You can get rid of this issue by removing corrupted patch related meta-data manually and restating the server, so that the server will apply all the patches form the beginning.
- remove [CARBON_HOME]/repository/components/patches/.metadata
- restart the server. (do not interrupt while starting up)