Red means there are non manifold issues. Maybe non manifold edges (more than two faces share a common edge) or non manifold vertices (where a vertex connects wrong, non logical faces).
This issue may happen when the CAD app converts its solid objects to a surface mesh file.
First: Make sure that the source app exports the surface only (not the whole scene which might contain some objects you did for construction purposes)
Then I'd try to export to .obj instead of .stl. Basically .stl is a non indexed format, simply a list of triangles. If there are triangles using the same vertices these triangles are welded on import. If there are duplicated triangles (e.g. if you made a duplicate of a solid and forgot about that duplicate as it is equal to another one) there might happen wrong welding. .obj instead is indexed. Means there's decent information in such a file showing the import application which faces to weld.
If the upper steps do not solve your issue: You might try ANALYSIS/Inspector which should detect several issues marked with red pins. These mean that MM isn't able to repair the error without changing the existing geometry. This might work but sometimes this will delete or deform (especially if that low poly as in your case) stuff. If Inspector's result isn't acceptable MM can't repair your mesh: Try another repair program (e.g. Netfabb or Meshlab).
