Could be. I know that when I want to change planets my small harvesters are routing back and forth too, I have to tap the little brown square next to the planet, select one of the auto pilot ships and tell it to cancel automation. I then go do something else and check back on it and it will be off auto.

Now thinking about it this might be because the ship has reached last planet route destination. If thats the case then the above would hold true and you wouldn't be able to stop a probe in transit. I'll have to start playing with my probes and see what happens.