The major problem is the influence of big corporations in funding studies and promoting certain points of view for their own benefit. This is a huge problem in the food industry and also the drugs and medicine business. If you look at the history of the popularity of vitamins, orange juice, the promotion of carbohydrates and sugars over fats and proteins etc. Not a problem with Science per se.
The underlying problem is an insufficient diversity in sources of funding for science. Scientists are people, and most just want as safe a career as science allows, which isn't very safe at all. Rocking the boat is, for them, a bad idea.