Description: TrailRunner downloads elevation data from a source that originally retrieved the data from NASA satellite measurements. What NASA did was to scan the surface of the earth and to record the topmost spot found during the recording. This could be the street level surface, a mountain peak or -- and that's probably what you are facing -- the top of a house or tree.
Solution: The error described comes from false GPS recordings. If your recorded GPS point is slightly off track due to a measurement error of your GPS, then the wrong elevation data point is being downloaded. Unfortunately there is no solution to this problem. Just ignore the spots where this had happened or correct the values by hand.
Hint: To correct values by hand, open the black info panel and manually enter elevation data value for spots that seem to be inaccurate.