Hi,
As you probably know, the link between the metadata (database), content store and indexes is maintained in a transactional manner. It is perfectly acceptable for the system to check the database for the existence of a store, and if not present, to go ahead and create it in both the database and the indexes.
If, however, the database was cleaned out at some stage, but the indexes were left in place, then the system will create a second root node in the index. Most probably, you cleaned the database out during some testing but left the index files lying around.
Regards