I'm getting the same error trying to delete users at the vCSA appliance level. Specifically this:
The "Remove permission" operation failed for the entity with the following error message.
Provider method implementation threw unexpected exception: %s
I suspect this is a bug since the exception doesn't show the actual error string, but instead the variable "%s".
I originally had the vCSA 6.0 appliance that I upgraded to 6.5 and I believe I added these users before I upgraded. Tried logging in as the SSO admin and it's the same error. I upgraded the vCSA to the latest version 6.5.0.5300, but that had no effect. I also tried to re-add the users (no errors) and then delete them (no errors), but then they still appear in the permissions list. If I attempt to delete again then I will get the above error.