Question

When i was waiting for the bus, TOM came__his father's car

Answer 1

When I was waiting for the bus, Tom came by his father's car.
当我在等公交车的时候，汤姆坐着他爸爸的车来了。

追问

为什么不可能是BY IN ，即when i was waiting for the bus .Tom came by in his father's car

追答

by表示乘坐的交通工具或者手段，所以我们经常说by car, by air/ plane, by bus, by bike等
而in则表示所处的范围，且这两个词在这种情况下绝对不能叠用，也就是说in his father's car不能做by的宾语。

Answer 2

in汽车在里面的。