Perhaps (and this is just a theory) it was Neo in the car, when all of the sudden an agent took over the bus, and headed straight for him.

Seriously though: What SEEMS to be the best explanation is that the bus came over the intersection. (Heading straight, not turning) And I know that you said the bus was turning onto this road, but it's the only possible way I can see this to have happened. He carried on straight over the intersection, and either the Bus or the Car skipped a red light. SMACK! Pin.