A protruding vertex when egnes are merged..?

I tried jumping straight into blender about a year back and didn’t make much progress. Now, I’m following basics tutorials in order to try and build a good foundation for my 3D modeling. At the moment I’m following the blender basics tutorial here
http://wiki.blender.org/index.php/Doc:Books/Essential_Blender/04.1.Mesh_Modeling:_Hands_on

When it comes to “closing the top” in the words of the tutorial, it tells me to first extrude the edges and scale them in a bit and finally, merge them at the center using Alt-M.

If I do it in this order, there are no problems. However, if I do not extrude the edges before merging them, the resultant vertex just out of the model.
I’ve attached a blend showing what happens.
Put the model in from-ortho view. You’ll see that the middle vertex of the bottom face of the object sticks out. Why is that?