Thanks for sending the logs across.
We've identified the issue as being a problem with the way we're handling PL/SQL objects in dependent schemas not included for comparison.
We've got a fix for this that will be in the next EAP build (unfortunately we don't have any timescales for that yet).
In the meantime, a workaround would be to make sure your comparison includes all the schemas that are referenced by the objects you want to compare (so, if you're comparing a table in SchemaA that references a procedure in SchemaB, make sure you include SchemaB for comparison).
Hopefully that should fix the problem - please let us know if it doesn't or if you have any other feedback for us.