Some people are allergic to a protein in wheat. when these people eat foods made with wheat, a reaction destroys the villi in the small intestine. what problems would you expect these people to experience?

If villi are damaged, their ability to perform properly is impaired.

The effects are two-fold. First, damage or destruction of the villi decreases the amount of surface area in your intestine available for absorption. Second, rather than capturing valuable nutrients from your food, they are excreted, increasing your risk of malnutrition as well as vitamin and mineral deficiencies. 
Other symptoms may develop such as anemia, fatigue, and bone loss. The malabsorption of nutrients further puts your body at risk for other conditions such as weight loss or seizures.

Genetic engineering is the answer.