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Looks like they may have messed up when adjusting the doors... I would get them to fix that for ya.
Hi Great Mazinga, we bought a 2012 Equinox this last January and have had the same issue with the scratches in the door jam and seals. The dealer says the doors are too tight and therefore dirt is being ground into the paint/seals.
I personally think its a design flaw and that if anything the doors are tight enough to keep the seal tight against the door.
Have you taken it in to the dealer? What did they tell you?