Average mph is calculated from what you input for distance and how long the activity is. This would be the same for running. You enter the distance of the running activity and the pace would be calculated for you. You cannot enter the speed or pace in manual activities, only the distance.
On my Forerunner 945 LTE, I often record Indoor Cycling activities while using a Stages spin bike at my gym and need to enter the stats from the activity after I save the activity on the watch. I enter distance recorded on the bike and my average speed is calculated for me, based on the total time of the activity.
Care to share a screenshot of what your activity shows?
