Pool and Spa
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I need to know what hot tub you have to give specifics. However, it sounds like one of two things:
1.) IS pump #2 the pump that is used for the normal filtration and heating? If so, check the filter progam time mode for the pump. If it runs constantly it could be on 12 hour setting to where it will run 24 hours. Also, once you turn the tub off at the breaker and turn back on it could be that you have reset the filter mode and it will come on a run for a couple of hours or it's default time or the time set (it will just change the time the normal filter starts to run).
2.) A relay is not working properly and is staying closed allowing the electricity to continue flowing and not allowing it to turn off. You can unplug the pump at the control center to stop it for the time being. It may work ok for a bit but more than likely it will continue to run improperly until replaced.
Check the filter program times first as that is the easiest.