It is possible these are two separate issues. I've seen MoI fill in shapes outside the lines. I suspect it has to do with how it triangulates the surfaces for rendering -- possibly a number precision issue at a high zoom level. When this has happened to me, the model was correct, the rendering just didn't totally match the model.

For the extrude issue, maybe try copying your curve, move the copy to the end of where you want it extruded to and use loft to connect them. Not sure if it will help, but it would be a different way to get the same shape.