Yes, the Patriots got permission from the Cleveland Browns for what they were doing but didn't inform/get permission from the League and the Cincinnati Bengals. That's the only infraction.
Of course, it's possible (but highly unlikely) that the League or the Bengals could have denied permission. But, the Bengals preferred to make it a League matter instead of just asking the Browns PR folks (where the filming was taking place) what was going on. That was their right, but I think they made a poor choice.