Does this error continue after upgrading? I would expect this error to occur if you visit some wiki pages while you are still uploading the updated files, and vw_Permissions_Model is already uploaded but not vw_Hard_Core.
There is no way to prevent that case on the code side. The only way would be to complicate the upgrade process more:
1. Disable the VaultWiki add-on.
2. Upload the new files.
3. Re-enable the VaultWiki add-on.
4. Run the VaultWiki upgrade script.
For convenience, admins can just do #2 and #4, but the trade-off is that there might be some errors while #2 is taking place.
Completing the 4.0.12 upgrade is supposed to remove the scalars from the database.