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This is obviously not expected. I have seen cases where the _DIFF view has returned 2 rows before, although never in production. It was the case that there was an issue with the optimizer. My guess is that a different SQL plan is being used within your application vs SQL Developer. The plan used for SQL developer is not selecting the thrid row for whatever reason. File a SR (most likely against the optimizer) if you need hits looked into. Are you able to reproduce this at all in SQL*Plus? The addition of the predicates will change the plan, and in this case, allowed the correct results to be returned.
I had the same problem after having imported a dump. only 1 row for 6 objects.