Ride operators don't stop trains unless there is an emergency. Usually when a train stops on the lift or in the block brakes it is because a train in front of it (in the next block) hasn't moved -- maybe because of someone needing help to get in/out, illness, someone didn't have their harness on right, whatever the case. It's called a "setup", and the computer automatically stops the trains so that they don't collide. The ride ops will have to restart the ride, no big deal, really. I've done it dozens of times on both coasters I've worked (Iron Dragon and Disaster Transport).
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Po!nt of View: A different look at Roller Coasters.
http://www.crosswinds.net/~justmayntz/thrills/