1. She is at the bus.
2. She is at the car.
3. She is near the bus.
4. She is near the car.
5. She is by the bus.
6. She is by the car.
7. She is in/on the bus.
8. She is in the car.
[Doesn't #1 mean #7? Doesn't #2 mean #8? Is each pair the same?]
# 1 means she's standing (or sitting) near the bus.
# 7 means she inside the bus
The same is true of 2 and 8.