Unfortunately, there is not really a way to do what you are trying to do. This is a difficult problem.
As long as the impedance on both bus routes is exactly the same, the Network Analyst Route solver will somewhat arbitrarily choose which one to take. We see this sometimes in cases where there are overlapping roads or loop-shaped roads where you could go either way around the loop. However, if the impedances are exactly the same and the route segments are going to the exact same place, then the route generated will end up in the same place and show the same travel time, so the results will be "correct". Unfortunately, if you are trying to generate directions, then you will see a difference in which bus it says to take.
I wish I had a better answer.