nich0lai- The paint probably looks lighter because you're polishing away all the contamination/etc. that's between the paint and your eye and also removing marring (which will make the light refract instead of reflect).
As for the damaged spot, if the original issue had thinned the clear then even "normally OK" polishing could have compromised what was left and led to damage. I've done stuff like that before and, well... [stuff] happens. Short of using an electronic thickness gauge every time you polish I dunno if you can avoid having an "oops" every now and then. Think of it as a lesson in living with imperfections as opposed to striving for literal perfection. But I *will* say that I woulda been mighty surprised if that happened to me, at least on anything other than my Mazda MPV (crappy build-quality/paint/etc.).
On the off-chance that it *is* just hazing, you could try further polishing with milder/better finishing products. If you do *not* luck out you'll make it a bit worse, but in that case you're looking at paintwork anyhow so I don't see any real downside to giving it a try.
Oh, and I'll offer a little gentle advice to consider getting some different products that will perform the way you want them to. If I read you right, you're considering the Nu-Finish polish to be better than the 3M product and that's, uhm, surprising. FWIW I always recommend 1z brand polishes for people who are just starting out (good for experts too

) in part because they're *very* user-friendly while also being effective. Sources for 1Z:
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