They all rust here and there. Mine did. Yours has more than mine, but it's just surface rust. It's not affecting the integrity of the structure. Even if you did nothing about it, it would take a very long time to compromise structure. That being said, what I did was go over the rust with a wire brush and got all the loose flakes off. I then painted it with Permatex rust converter. Once that dried for about 24 hours, I applied Daubert Nox Rust, which is the factory wax coating. It looks brand new.
One question in your situation is what product did they spray on your frame. Some of the products degrade the factory wax protective coating and actually leave your frame exposed.