If the Humanoid Swimming State is disabled whilst under water the character will continue to swim. It will only stop swimming once the player has emerged from the water.
I expect a check is being missed when the swimming state is disabled to see if the character is currently underwater & swimming.
My use case for this is that I want to create a submarine. If a player swims through the door I will disable their Swimming State. However this isn’t possible at the moment because they are already underwater and will continue to swim.