I have spoken to enterprise support with Apple and this is a known issue. This is more likely to happen if your app library is over 3 GB.
Here is the fix:
- Uninstall all your apps
- Reinstall each app in batches of 4–5
- Once you discover the problem app, redownload the VPP spreadsheet for that app. You then want to reimport it by clicking on the # to the right of the app.
- Finish installing the apps in batches to make sure there are no more problem apps.
Again, this is a known issue.