Algodoo

OOhhohohh I know why the extra space appears

The red triangle is'nt at the same angle as the green. It's surface rises slower and so makes a hole when you put it on the top, since when on the bottom, the bottom area is less high than if you put the red triangle on the top, so the hole fills. When the green triangle is on the bottom, then its slightly highter and so "lifts" a tile out of the hole

Yea.
The triangles are slightly concave? or convex? (I think)
And the hole accounts for the missing square.