We have had the same errors after upgrading to Mx9 from Mx8 and Mendix Support told us the following:
To answer your question, System.UnreferencedFile is internal bookkeeping for keeping track of external files which are not referenced from a FileDocument, but which cannot be deleted yet, because of open transactions and possible rollbacks.
Regarding the error, it's known to us that is caused by an internal process that runs every ClusterManagerActionInterval (a runtime variable). By default, the interval is 5 minutes, which causes this error to be thrown every 5 minutes. The message indicates that a FileDocument was not deleted because of a safety guard Mendix put in place. However, this should not happen. The way we identify files changed and a switch to a new File ID was made. The error is caused by using the ORM.cloneObject of a version of the Community Commons module to create a copy of a FileDocument which was not yet compatible with the change in the File ID. This was resolved with the release of Community Commons v8.5.0 but by using older versions there can already be 'wrong' data in your database that now causes this error to be thrown. The following steps can be taken to resolve this issue:
TLDR: delete all rows in system$unreferencedfile if you don't want to get the error anymore. However, the underlying cause is a mismatch between the FileDocuments in your database and the actual files on your fileserver. So a proper solution would be to resolve it there before cleaning the unreferencedfiles.
I have noticed the same issue as well. Could this cause automatic restart?
Restart started recently and is caused by great amounts of logging.