Perhaps it may be because some of the normals aren't facing the right way. Go into the menus of MED and look for a configuration setting for the 3D view to draw backfaces. Backfaces are untextured and have a dark bluish-gray color by default. If you see such faces that shouldn't be like that, go into face mode, select those faces, then click the "flip normals" button.

It could also be that you haven't built some of the faces or they were built incorrectly (from which you'd see in the 2D views as triangles going to odd or unusual areas and would stick out quite well).

If otherwise, please post a screenshot of what you're seeing.