Difficult to see what you have going there - if you could post a wireframe view it would help in identifying issues.
Try this - with the object selected in the properties panel, go to the top menu -> Selection then select in turn - Select over-4-point faces, Select non manifold edges. If anything gets selected, you have a problem - let us know what it is.
Also look for reversed normals - with the object selected, go to Utilities->orient normals. That should show you a lot of red arrows, all facing away from the object surface. It is difficult to spot any faces which may be facing the wrong way, so hit the A button, then the “unify normals” button - you should get a single yellow arrow pointing away from the surface. If it is pointing inwards, hit the A button again.
See if that fixes the problem.