This bit me this morning... I added an application to INSTALLED_APPS but forgot to include it in TENANT_APPS; when I started migrating the migration code was not being executed, although the migration was being marked as processed, and even recorded in the database.

Ultimately though this is an error state - an application that isn't allocated one way or the other can't be migrated because we don't know if it is intended to be in SHARED_APPS or TENANT_APPS. Guessing or defaulting is worse, so I think the best solution is to add this to the system checks.