Did you assign train 482S before the scheduled entry of 482Sa?
You must assign each arrived train to its corresponding transfer train to the depot,
otherwise the transfer train (482Sa in this case) won't have a way to enter the layout,
thus "derailing".
In this scenario the author chose not to put a Wait: instruction on the transfer trains.
He only put a Stock: instruction on the arriving train.
Maybe that's the source of the confusion.
Also, I suggest you try to move the transfer trains out of the way by shunting them
instead of waiting for their scheduled departure.
This scenario is a lot of fun, with all the passenger trains coming in while the freight trains
have to wait on the side tracks. Never a dull moment!
Have fun,
Giampiero Caprino