Each locomotive on your railroad has a mobile decoder which receives the command control signals from the command station and operates the locomotive motor accordingly. The performance of mobile decoders can be adjusted by changing the Configuration Variables (CV's) of the decoder. You can improve the speed performance of a locomotive by adjusting its start speed (CV02, V-Start), its mid-range speed (CV06, V-Mid) and its top speed (CV05 - V-Max). You can also adjust the acceleration (CV03) and the deceleration (CV04).
If the deceleration CV value you set for a particular loco is very large, this can make it look like the loco is not stopping on command because the deceleration CV value is causing the loco to take a long time to come to a stop. Likewise, if the locomotive isn't moving, it may be because you have inadvertently set the value of CV03 so high that it takes minutes for the locomotive to start moving even though the throttle is wide open.
If you have a loco that seems to be having trouble starting or stopping on command, you can either go back in and adjust the values of the problem CV's or reset the decoder entirely.