First, tell us what kind of throttle you use (specs)
Do a quick test just to get some basics..
in case you have a brakeswitch connected (mind the difference between NC and NO switches and that you used the correct one!)
hit the brake and see if that stops the motor.
if you don't:
push the throttle down (say half way if that's what let's the motor spin for you)
and release it.. now pull the throtle back manually (not simply by spring tension)
if the motor still spins, disconnet the throttle!
Does the motor still spin now, w/o the throttle attached or the brake switch triggered?
If so, you might have a controller with a "coaster" switch
that sets the motor speed with the throttle and KEEPS that speed once the throttle is released until you hit the brakes.
untoggle the coaster switch.
If you used a potentiometer throttle you might have a faulty controller
(weirdly conducting cap perhaps *shrugs*)
but to me that sounds that you accidentally connected a coaster switch
(say thinking it'd be the speed limiter or so)
or a gunked up throttle which doesn't reset to it's starting point properly,
that's a matter of good mainetance only (clean and maybe a pea of grease can fix that one

)
'sid