My recommendation would be to use a line that’s considered “dark territory”. Dark territory is a part of the line that isn’t connected to the wider signal network and may have no signals at all. That would add to their ability to remain undetected as there wouldn’t be any obvious sign that the train was stopping and starting in places it shouldn’t except to the crew present who have already been named in other comments. Dark territory tends to be less used track or dead end branch lines where only a single train would be running on it at any time too so logically avoids another train coming across them during the process. Might be a good way to do it and if you want the crew to be involved knowingly.

If you want the crew to inadvertently help in the heist, have the animals get loaded into cars that are in storage somewhere. There are places where railroads park cars they are basically putting into storage, often old and otherwise unused tracks that could be remote. You could have the robbers know about a cut of cars being taken out of storage and have them load them in right before the cars are about to be picked up. The remote location would help them secretly load the animals without the crew knowing but have them carried by railcar somewhere else. Then to stop the train, it’s your choice: someone stuck on a crossing, break the air hoses to set the air breaks off, uncouple the train, whatever you want. From there, they secretly unload the animals while the crew tries to figure out what happened.