Additional filtering so that permissions changes on objects can be ignored.
Add an option to the filtering so that different aspects of objects can be ignored, e.g. ability to to ignore different permissions on an object.
We have one database that has permissions set individually on objects, and another database with the 'same' objects, but they don't have any explicit permissions set, but SQL Compare consideres them different, so we currently have ~1700 objects with differences that are only 'user x has y permissions on this object'.

The ‘Ignore Permissions’ option (Options→Ignore→Permissions) should do this. If it’s not working for you, please e-mail support@red-gate.com
If you need more granular ignore options, please feel free to add a new uservoice suggestion with the details.
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Nick Kroes commented
I agree with this suggestion. When comparing our production database to our QA database, the permissions are different even though the objects are the same and SQL Compare attempts to generate a script to drop the permissions on our objects in production.