Bad bus route design I would say. I've had busroutes with busses filled completely with passengers at that population.
Tips:
Make your busroutes cover the busiest driving routes. If you use the traffic report mod (I think that's the name) you can see which routes are heavily used and then you build a bustoute to cover that.
Also don't build you're routes too short. I usually start building relatively long routes and when these get too busy I will add bus routes and eventually split some.