There are a couple of potential sources for the marks. One is grease from the bag belts, cargo doors, etc. Another is broken down rubber and gaskets.
I would hazard a guess in your case it is the later, broken down rubber, which can be very sticky and hard to get off. Rubbers, exposed to heat, sun, time, grease, human oils, break down and become a gooey mess (ask a cyclist what the rubber covers of their brake levers are like after many years of use). Rubber gaskets, bumpers and seals are used in many aspects of the airline baggage handling, so easy to come in contact with your bags.
The easiest way to remove them is with a solvent type cleaner, alcohol, turpentine, even gas from your lawn mower. Commercial products like GooGone that Zach mentioned also work. And even better the same solvents will remove grease as well, just in case you encountered option one.
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