I know this doesn't help fix the problem at hand, but my suggestion is to constantly check your work as you go. It does you no good to spot an area that still has swirls
after you have put your final layers of sealant and wax on the car. By checking your work as you go you won't run into this problem.
The faded area could be oxidation, although that seems unlikely for a car that was just polished. It could be hazing from your polishing pad. What type of pad did you use and at what speed? Sometimes I find it necessary to step down the polish and/ or pad depending on how severe the damage is. For example... Here is a a hood with swirling on it before polishing:
Here it is after polishing with Pinnacle XMT 2:
Can you see the hazing and cloudy appearance? Plus there are still some swirls. So I step down the product to XMT 1 and go over it again. Check it out after a few minutes with that product:
After a couple more passes with XMT 1 the hazing and swirling were all gone. Now I knew what I had to do on the rest of the car to get the same results. I still checked my work with the 500 watt halogens on every body panel before switching products, but I knew that what I was doing was effective and the final product would be awesome.
Anyway, that is what I would suggest for you. It is possible that you have hazed the surface with whatever pad you were using. I would suggest perhaps some Meguiar's #83 (DACP) that has diminishing abrasives and will polish it's own hazing out fairly well. Here is a hood that was only polished using DACP and a PC:
Before:
After:
No haze and no swirls. DACP is a good product that is easy to locate in town if you can find a Meguiar's distributor. Check your local auto body paint shops. They sometimes will carry both 3M and Meguiar's products. Hopefully this helps a little.