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

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?