MSC Verify can search the database quite thoroughly when it is performed. When warnings and anomalies are returned from the verify log, it does not mean that the database is in an unusuable state. A couple of common checks include:

Orphan methods
These are object methods that belonged to a form which no longer exists. To resolve the warnings, simply delete the orphan methods via Explorer > Methods

Trashed forms and methods
Warnings and anomalies also search for issues in deleted forms and methods. To resolve these issues, simply empty the trash via Explorer > Trash