Well, the fact that she told you to stop running without explaining her reasoning is a little weird. But I've read a few articles regarding how exercising can actually make you fat.

This is one of them: http://nymag.com/news/sports/38001/

This article is 5 pages long, so I'll try to summarize it. Basically, every time you exercise, your body releases hormones which will make you feel very hungry. This will cause you to go home and eat more than you usually do. So a lot of people who will rely on exercise alone to lose weight (or lost weight then rely on exercise alone to maintain their weight) will fail. A change in diet is necessary for a person to lose weight, and exercise should compliment that diet.

So I don't know what your diet is like, but as long as you watch what you eat, count your calories, watch your carbs etc etc.. I don't see why running is bad! Specially since it's a stress reliever.