My friend has a sore throat, stomach ache, headache and fatigue. He got the flu shot a few weeks ago. Is it allergies? A cold? What could it be?

Many possibilities. Not the flu unless he was already in the early stages. In the flu shot the viral genetic material has been denature or "killed." your body will probably react with mild symptoms because of the remaining products used in you immune response. The responses vary on how fast your immune system responds. Could be many causes .. Least of which is the flu.