I had the same thing happen to me on Boston sprinter i was routed through a building in the yard near Boston station
It also appears that some of the collectables might be unreachable according to one of the steam game guides
Gameplay authored before the scenery is added no doubt. Some sort of marker system for these buildings with through tracks could be implemented at the track laying point so that the gameplay team don’t put trains through them.
Certainly seems so. Especially considering that a significant number of the buildings were only added after the first preview stream.