The judge decided to make him pay because he painted over them before the previous ruling came in place. There was like a law that if the art attracted people or something like that, that you needed a permit before painting over it. The guy painted over it before he got the permit (which he did get btw) and thats why the judge ruled in favor of the artist.
But continue to get upset because you dont understand the laws.
The judge is trying to apply a specific law to a privately owned building. The permission he was talking about was the owner painting the building while he was waiting for the demo permits. He literally is super offended in his decision that this guy denied fans 10 months to admire the building before he destroyed it. This isnt a historical landmark in a true sense and should have no protection.