Interesting. What you've done is found a roundabout way to create an "illegal" shape. Try this: select the final weird shape and delete it. Now, select all the points and try to create a shape - Moho will only allow you to create an outline, not a fill.
This is because the filled shape is "illegal" - it has undefined boundaries. It seems clear to us what parts should be filled, but to Moho it's not at all clear. So, when you try to fill the shape, Moho just won't let you.
However, by first creating a legal, filled shape, and then modifying it to make it illegal, you found a sort of "loophole" that lets you create invalid shapes.
During beta testing for Moho 5, we tried out a feature where illegal shapes like these would be automatically deleted. However, this seemed really confusing to users. I'm not sure what the best solution is - I gues just "don't do that".