Do you get the same effect with just a simple cylinder? If not, then I'm guessing you've done something weird with this model, and you may want to re-create it.
How did you create that portion of the model in the first place, as two halves? Are you certain you don't have any overlapping or duplicate meshes? Or maybe flipped faces? Are you using two-sided materials?
The process was following:
1. i've done a simple shpere,
2."convert to mesh"
3.switching to point edit mode and removing some points from top and bottom of the sphere
4. used non-uniform scale by axis Y
I'm receiving the same effect everytime when i'm creating a simple cylinder or sphere and after that convert them to mesh
I'm using a one-sided material, the normals are the same (i've exported the model to the orbiter flight simulator - if normals were reverse, there will be seen a hole in place of the reverse normals)
I can send this part of model if needed...