I remember that some older versions of XWiki did not clean up the information about a sub wiki from the extension repository when that sub wiki was deleted. As that bug has been fixed in the mean time creating a sub wiki with the same name and then deleting is indeed a clean way to fix that issue.
However I also noticed that when copying sub wikis (i.e. creating one subwiki from another one marked as template) will create the pages in the new wiki with authors from the original wiki. This will cause problems as the (local) users from the template wiki have no rights in the newly created wiki.
Even more, if the original template wiki is deleted, these pages will have non-existing authors. This might have created error messages like the ones described above.
To make sure that all references to users from a deleted sub wiki are removed (by converting them to local user references) I have written a snippet:
Replace page authors from another subwiki
You need to type in the name of the deleted sub wiki in the code of the snippet and then you can first check if such references exist and decide to repair them. I hope this is useful in your case.
Aside of that I have observed that in XWiki version 13.10.3 deleting a sub wiki creates an error message at the beginning of the creation process when creating a new wiki. This error does no longer happen if one restarts the wiki after the deletion.
I have not been able to track down the source of the problem; however with XWiki 14.6 it is no longer reproducible.
In any case none of these errors should endanger the stability of the wiki server as a whole. These are only errors when accessing no longer existing data in some circumstances, which creates these spurious error messages.