I understand that some players prefer changing a schedule while the vehicle is on halt, for example if you don't want the current load to reach the next station. But the traffic jam caused by this stop can lead to more trouble then one more load of goods at the wrong place, if making the changes takes you too long, especially when trains are involved: one train stopping in the middle of a track can cause a whole cascade of none moving trains because of signals that make the following trains stop.
I see several possible solutions to this problem:
1. Player must create a complete new schedule first, and then assign that new schedule to the appropriate vehicle, instead of changing the current one.
2. Put the whole game on pause automatically, whenever the schedule of a vehicle is changed, so there won't be any blocked roads and tracks. That function should be optional, of cause.
3. On roads, make the halting vehicle stop a bit to the street's edge and let the following cars overtake it. That won't work for trains, though, unless you send the train onto some virtual holding track.
I agree that this is not easy to solve. But at least, don't stop the vehicle as soon as the player opens its schedule tab. Some times you just want to take a look at it. If a stop is unavoidable, do it as soon as the first change is made.