Invisible non-manifold lines I can't fix

I’m new to Blender and am learning how to create avatars. I’ve just gotten to the unwrap and texture stage but I saw these spots on the head that I couldn’t texture. I found out they are turning up as non-manifold edges. I’ve gone in and done everything possible, everything I could find online, but it seems as though there isn’t anything wrong with the geometry outside of just not being optimal design. Theres no doubles, normals are fine, I’ve deleted and rebuilt all the edges and vertices reporting as non manifold. I don’t know what to do.

I just now used an add-on called 3D print which detected and fixed the non manifold edges but it did so by creating stretched out impossible internal geometry connected one vertices all the way to the back vertices. I’ll provide pictures.

This is the effect of fixing it with 3D print. A worse result than I got the first time, it deleted the geometry under the chin and stretches out the inside geometry to impossible places. But Blender recognizes it as proper.

Heres the non manifold edges.

These lines appear in object mode but there is no such edges in edit mode that I can select. This spot wont allow me to texture as well as the non manifold areas. This specific spot is not marked non-manifold, but what are these lines? Its not doubles, I’ve checked for that and totally deleted all geometry in this spot then rebuilt it.

For further context, I used a subdivision for most of the modelling but didn’t realize you had to apply it. I applied it late in the modeling.

I’m limited in the amount of images I can post apparently so I can only go with these.

I believe it actually is possible to get an unfixably broken geometry (probably due to hitting a bug in Blender). What you can try to do then is to duplicate as much of the mesh as possible (such that the duplicate does not contain a copy of the defect) then use Mesh->Separate->By Selection to split the duplicate out into a new mesh object.

I managed to fix them somehow by merging the mirror and just deleting and remaking them till they stopped showing as non manifold. But then I’ll start a new object, a simple one and for no reason it shows parts as being no manifold, its actually getting pretty frustrating because I know there is no issue with the geometry.

Just can say, I encountered similar issues occasionally. Apparently there is bug somewhere (or at least has been in certain versions). If one could figure out a sequence of operations which reproducibly create such a defective mesh and file a bug report about it, people would be thankful I guess. Unfortunately for me it only ever happened after a lot of editing.

You might also upload the .blend file from before you fixed it by trial and error, maybe someone will find the real/underlying issue and a more solid way to fix it or avoid it.