OpenSCAD "not valid 2-manifold" useful information
Occasionally, a model created in OpenSCAD will have, as you suggest, overlapping segments. Often enough, this will generate the message you receive. OpenSCAD has an implied union function when it comes to independent objects, but if you wish to clear those errors, experiment with explicit union statements where you have joining objects. It may be necessary to join only one pair at a time to clear the error.