From my experience it a combination of things, but I believe it is mainly the phenol acids that are produced from buring wood which are carried by the smoke and deposited on the food. also the salt in the rub are the main factors for me. I don't use CT or vinegar based sauces on my brisket, and if I store my brisket in foil pans for a short period of time I will see a lot of discoloration of the pans. If I wrap them in foil, the foil will begin pitting within 12 hours. For storage I always wrap smoked foods in plastic wrap first, then foil. Or as suggested use plastic or glass containers.
The aluminum in the food is not harmful, but too much will add a bitter taste.