[abenedik]

I do not know what is expected and what kind of meshes you use. Maybe the problem is that the 3D printer do not like that there are parts of one mesh inside the other mesh (this happens because triangles are just merged and no regular Boolean operation was performed).

I would advise you to merge two simple boxes so that they will intersect and try if the 3D printer would complain. If this will work well, then try to find the problematic mesh by skipping different meshes when exporting.