Great one! I'm glad I can answer a question for you. This can be caused by deleting/changing a file while it is open. Mine specifically was /usr/scripts/callfixsub31.sh. The inode was still attached to the running process. You/I started the delete process, which could not be comitted until the inode was released by killing the offending process.
Chances are, in your case, the app was running?. The mod changed the inode which placed it in limbo? The readonly copy was still attached to the process and your new inode could not be comitted?
Not a bug but a feature. This allows you to make many changes to a live OS and reboot. Even if the processes won't willingly die at shutdown, the OS will kill -9 everything before unmounting the FS as cleanly as possible. We hope.