I suspect an issue with the grouping of the stops. Or perhaps we don’t understand this concept well enough?
It can be an issue with grouping, changing a line attached to a grouped stop will recalculate all lines which go through any of the stops in the group. Try un-grouping the stop’s in question.
Hopefully way points will solve it, its still a hassle, especially with 5 track train stations, which of course, you can’t un-group
