Can you feel the scratches at all with your fingernail? If so, odds are they are indeed too deep to safely remove as doing so would involve removal of too musc surrounding clear coat. If you can just barely feel them you might be able to correct them with some light wet sanding and compounding to remove the resulting sanding marks. But be warned - this is a very advanced process; if you've never done this then this is NOT the time to learn!

At this point I'm actually much more concerned with what the body shop might have done to the finish when you had them buff out the whole car. Body shops and detail shops have vastly different mindsets and disciplines when it comes to this sort of thing. Just as I would never let a detailed paint my car, I'd never let a body shop detail my car. My big fear is holograms left by speedy use of a rotary buffer. No prmeanent damage, and certainly nothing that couldn't be fixed, and I hope I'm wrong. But I'm also the most nit pichy SOB you'll likely ever meet on the subject, given what I do for a living.