In at least two 7.9 projects, there are appearances of the compound nodes of documents at root level.
In one case, we suspected the renaming of a document to be causing it, but that was not confirmed nor reproducible. Another suspect was copying a document. In the other case, we're in the dark, there we're not a lot of renames in the audit logs.
In fact I'm not even sure it's a repository (SCXML?) issue.