Flaking aluminum foil

According to the North Carolina Cooperative Extension Service, there are 2 reasons why aluminum foil flakes or "pits":
1- when aluminum and a dissimilar metal such as silver, stainless steel or iron are in contact in the presence of moisture, an electrolytic reaction may occur, causing a breakdown of the aluminum. To prevent this reaction, use plastic wrap (as other posters have recommended) to cover non-aluminum metal containers used to store food.
2- the other cause is a chemical reaction--heavy concentrations of salt, vinegar, or some other acidic compound, or highly spiced foods can cause the foil to disintegrate.

The product of either of these reactions is an aluminum salt. It is not harmful but should be scraped off the food as it may impart an undesired flavor and color. Hope you find this as informative as I did.