When programs open a file they put a filesystem lock on it to prevent other programs from editing the file at the same time. This is usually a quick lock so the file can be read into memory, and then the lock is released; however, there are times when a program needs to maintain a lock, or times when a bug might prevent the lock from being released. When this happens if you try to edit or delete the file the system will not allow it and will issue you the "in use" error. Fixing this requires quitting and relaunching of the application, but if you cannot figure out which application it is (or if it is a background service in OS X), then as softwater mentioned the easiest solution is to reboot the system. This will cause all processes in OS X to release their filesystem locks and re-initialize, and therefore clear the problem.
The "Resume" feature is separate from file locks. Resume just stores a document/window configuration for each program and will read this to restore the workflow as-is (using auto-saved files, etc.) when the program is next launched. The file lock issue happens below this, where any time an active program accesses a file (be it in an auto-resume configuration, a user-opened document, or otherwise) it will place a lock on it while the read/write process is happening, and then should release this lock if programmed properly.
Shutting down or restart/rebooting will do the same thing with regards to the file locks. Both processes will require all programs to quit and thereby release any current file locks they may have.