It looks like there’s little demand to go from stop A to B, there is plenty from B to A2 and the other stops, but passengers still use A to go to B just not as many as A2 to E.
I tested the map and it seems that the time to travel from the entire route from A to B is pretty long as it is technically the last stop on the list. The game picks A2 as the “true” starting stop as it covers the inter city lines then A is considered an outbound stop as it connects to B.