DBCC CLONEDATABASE missing schemas
Sounds like you had objects in SQL Server 2000, and their owner was dropped, leaving those objects "orphaned." When the database was upgraded to any version >= 2005, the "owner" was changed to a schema_id, but for those owners that had been dropped, that schema didn't exist.

To fix this, you can create a bunch of dummy schemas until you have one that correlates to each missing schema_id, and then run a statement like this for each object in each missing schema:

ALTER SCHEMA dbo TRANSFER dummy_schema.object_or_synonym;


The only complication might be if you have objects with the same name but different schema_id values; these will collide. Once you've sorted it all out, then you can drop all the dummy schemas. 

At some point you might consider creating a new empty database in a modern version, copying your tables and data to it, and then getting rid of the old one. Might eliminate more surprises like this in the future.