Hey I had the same problem with a white Commander I purchased in Florida. It had black specs all over the bottom portion of the door panels on one side only. It also had yellow stains on all four fenders and the sides on the rear plastic bumper after they detailed it, so I returned it to them and they kept it for a week. They had to replaced the fenders but said they forgot to remove the black stuff off and the dealer wanted another day to fix it. I don't know if they ever did cause I gave the Commander back to them and took my $1000 down back and bought a black one from another dealer.
I don't know if they can get it off but if I was you I'd ask for another white Commander or change colors cause the white seems susceptible to stains. I couldn't find anything either to take the black specs out and it seems the dealer couldn't either. Good luck.
2006 Commander 4.7L 4x4
Gone but not forgotten!
2000 Wrangler Sahara w/3" Teraflex lift, DT3000 shocks, warn winch (which I still have, I'm not completly insane), Teraflex QD, 33'' Dunlop mudrovers and ORD rock rails.