To fill one car, it is important to fully load two crates that are placed right next to each other. If there is a gap between them then they are not part of the same car. You can receive rewards and player XP for completely filling individual crates, then receive dollars and cargo train XP for filling 2, 5 and 7 cars. If you fill 7 crates in 7 different cars then no extra rewards will be given when the train departs.