Go into the tracks and boundaries view of the map project and look at your track points. It might be obvious here where the problem is, but if it is not then open the Tracks section of the Edit panel and adjust the depth range using the sliders. This should help you find the bad track points, which you can then remove. You can remove either individually (right click, delete), by doing an area selection or by using the depth filter. Note that if you select an area first and then use the depth range filter, then only points within the selection will be filtered. If it is just one or two tracks causing the problem, you can remove them from the project by using the option in the right-click menu of any track-point within the track. It is also possible to adjust the water level offset of a track if it is a water level issue.