If you're not nourishing yourself properly prior to the run, then yes it can. One, you are burning calories that your body could otherwise use to increase muscle mass. Two, you are throwing your body into a catabolic state, which means that your body may start eating its own muscle. I usually try to eat 30 minutes before I go jogging, and then again immediately afterwards. However, if I were you, I wouldn't jog for more than about 30 minutes if you are trying to gain muscle mass.
You should do a search for HIIT cardio. This form of cardio will speed up your metabolism quite a lot and is less likely to induce catabolism because of the shorter duration of the session.