I often get the question as to why we have this error when using an incremental Content Deployment: The specified file is already in used.
Simply, that message appears if the authors have created a file, deleted it, and recreated another file with the same name. All that before a single incremental content deployment (or Quick Deploy for that file) has occured. Basically, the incremental will process the "delete" action after the "create" action and that's the standard error for that. Fortunately, the deployment job will keep going as it's not a fault error; unfortunately, you'll have a 404 when accessing the document.
If you do not want that issue, simply overwrite files instead of delete+recreate. Otherwise, you'll be stuck having to use Full Content Deployment all the time.
**UPDATE** : The new WSS post-SP1 rollup, KB941422, may contain the fix as it seems to fix a similar issue when you recreated a deleted list. I'm hoping it works for list items as well. **/UPDATE**