Sounds like either an irritation to the lateral Wikipedia reference-linkmeniscus and or an ITB issue. Both are going to be related to the way you are running and really you need an assessment from someone to see why you're getting excessive joint forces on that side of the knee. The shows you'd wear for fell running should probably be more supportive and those you wear for running on the road. Perhaps that is a consideration as the uneven surface of fell running require a lot more hip stability so as not to place excessive loads on the knee.

Go to a good local sports physio and get a gait assessment and while you're there they can see what structure is being implicated. Remember it is likely that discomfort is a symptom and the problem may lie elsewhere.