Probably a little bit of both,
@rhban. The station script is supposed to control where the train stops, but many of the changes made lately in preparation for The Living Railroad and other upcoming features have broken (or at least severely bent) many existing assets. Some interaction between the two probably controls the actual outcome. As
@stagecoach mentions, some of those changes may have affected the triggers used by the stations, and those trigger setting also affect the stopping location.
Just curious, when this occurs multiple times within a session, do the mis-placed stops occur for all engines at a given station, all stations for a particular locomotive, or apparently at random? Does this occur only for a specific instance of either one, or for all instances? In other words, is there any discernable pattern to where and when this occurs?