We have started noticing the following warnings during back up of some sites.
Processing site https://<mytenant>.sharepoint.com/sites/<SITE> finished with warning: Failed to backup list: <Document Library>. File not found in the database (ID: <Some Guid>, OwsHiddenVersion: 1)
For one document library the issue seemed to be a new file that was uploaded and the required metadata wasn't populated yet. Once populated and the file was checked in, the error went away. However, I am now getting a similar warning on another document library but this one doesn't use Check-in\Check-out or require any metadata. It's just a default document library.
First, please let us know your support case ID. There might be a variety of reasons causing such an error, and it's hard to make any conclusions without seeing logs and details. For example, potentially this issue might occur when backing up an item with an attachment, and if it's the case, you could either get the fix from support or upgrade to the new version 4c. But again, I'm only guessing for now.