I think you see that when you add a stop it says "x minutes / y miles off route" so it's obviously trying to take you as quickly as possible off the route from A to B, because if it was doing A->C then C->B then C would not be off the route as it's clearly on the route!

See this thread.

Routing servers have been giving bad routes for weeks now (especially for stops). I get a bad route every morning for my commute at the moment.

So there is probably nothing wrong with the map.