Not sure if Diff and DB Copy share the same code, but there are already two bugs logged for this issue against DB Copy:
Bug 13619659 - DB COPY: FORUM: COPY DB CAUSES ORA-14652
Bug 13646884 - NEED TO RESOLVE THE DEPENDENCY ORDER FOR TABLES CREATION
Current status: this is being treated as an enhancement request approved for a future release.
How well DDL generation handles dependency order may depend on your SQL Developer release (not mentioned in your post). Please trying upgrading if you do not already use the latest production release, 3.2.20.09.87.
SQL Developer Team
Apologies, it has now been deleted so I can no longer edit.
I was simply aiming to provide a solution to the question "Or is there a better way to migrate changes between schema's/databases?", hopefully the user is able to find an alternative.
It would be good to read guidelines for the forums, do you know where they live? All I can find are the FAQs here https://wikis.oracle.com/display/Forums/Forums+FAQ