Why does foil sometimes darken, discolor, and leave black specks on food?

The darkening may be caused by moisture from a food being covered.  It is the result of a buildup of aluminum oxide, a totally harmless substance. 

Occasionally, foil comes in contact with a different metal or a highly salted or acidic food and, as a result, pinholes develop in the foil.  This reaction does not affect the safety of the food.

Source(s):

The New Face of Reynolds Wrap Foil  “Frequently Asked Questions”

http://www.reynoldspkg.com/reynoldskitchens/en/product_info_page.asp?info_page_id=743&prod_id=1789&cat_id=1337

General Guidelines for Wrapping Foods

What’s better for wrapping food—plastic or aluminum foil?

What produce needs to be wrapped before refrigerating?

Should I wrap raw vegetables loosely or tightly before refrigerating?

How should fruits be wrapped before refrigeration?

Can I refrigerate meat and poultry in its store wrapping?

How should food be handled and wrapped for freezing?

Using Plastic Wraps, Bags, and Containers

Are some plastic wraps more effective than others?

Can chemicals leach unto food from plastic wrap or containers?

Are any plastic wraps or containers really “microwave safe”?

Can I use plastic freezer bags to store produce in the fridge?

Do coated plastic bags really help produce last longer?

Using Aluminum Foil Properly

What are some advantages and disadvantages of aluminum foil?

Does exposure to aluminum cause Alzheimer’s disease?

Does aluminum foil give foods a metallic taste?

Will a foil cover help keep foods on the table hot or cold?

Is it safe to use aluminum foil in a microwave oven?