Remove a verticle in a tricky place I didn't know how to describe my problem in the title, so I'll try to do it here. Below I have a project. I needed to take a small piece from the middle of the object, and I couldn't get sculping to work, so I just used knife tool and excruded after I had created what I wanted. 

Now, when I'm finally rendering, I'm getting unwanted things on the render result, caused by these extra verticles. Is it possible to remove them? I tried making the holes new objects, but that didn't really work.

Oh and, with 'verticle', I'm refering to the line that connects the hole into the rest of the object.

http://www.filedropper.com/blend1 (a link to the blendfile)
The top and bottom vertices are missaligned.

Select all the top vertices and tyoe these letters: 

 s ,  z ,  0  "Numpad zero". Not at the same time.

This will aling all these vertices in the Z axis.

Repeat these steps at the bottom vertices.

See the image below: