Smokenque, I have had that happen to foil as well. Once I had put a couple finsihed butts in one of those cheap disposible aluminum pans and into the fridge a couple days, when I took the butts out the pan bottom had several pitted spots, which made me wonder about the safety of holding food in them. I found this information on the Reynold's foil website - section 2 gives an explaination.
Why does aluminum foil sometimes melt and leave black specks on the food?
Occasionally when aluminum foil comes in contact with a different metal or a food that is highly salted or acidic, small pinholes are formed in the foil. This is a harmless reaction that does not affect the safety of the food. It is difficult to predict, but may occur under the following conditions:
1. When aluminum and a dissimilar metal are in contact in the presence of moisture, an electrolytic reaction may occur causing a breakdown of the aluminum. To avoid this use aluminum, glass, ceramic, plastic or paper containers. Do not cover sterling silver, silverplate, stainless steel or iron utensils with aluminum foil.
2. A similar reaction may occur when salt, vinegar, highly acidic foods or highly spiced foods come in contact with aluminum foil. The result of these reactions is a harmless aluminum salt. Some aluminum salts are used in medicines to treat stomach disorders. The food can be safely eaten; however, the aluminum salt particles can be removed from the food to improve the appearance of the food.
Reynold's FAQ