Issue with the Connect Line Tool

[micheus]

When connection edges you must have pair of them - let say this way.
In a situation like that you show in the picture one that is the result. What you should have done was to select the large edge and press [2] to cut it in the middle; then you could select the respective vertices and connect them.

But, I noticed that your mesh still have other problems:

I just selected the top of your car and moved it up and I could noticed your model had more edges overlapped. Also, in the front and back side of the car there is some strange diagonal edges which result we can notice it by using Smooth Preview [shift+tab].

So, as you just started, I suggest you start it from sketch again. I don't know if you were follow any tutorial, but there is one very similar to your that could help: Box modeling a car with all Quad topography