It sounds like you may have a siphon related issue and the sensors have alerted you but thats all that they can do for this type of situation..
Look at this diagram/article here..
https://en.wikipedia.org/wiki/Siphon
As you see there if the water in the left tank is higher than the right tank and your tubing is like that diagram then the first time the ATO turned on and your pump started the siphon started..
The sensors may have stopped the pump but if the siphon of water which is now started and the water does not need a pump anymore to keep flowing kept going then the water will keep flowing until something breaks the siphon.
Some pictures of your setup from the side showing heights and then how you have the siphon break installed may help..
That or you can physically test the ATO by lifting up the ato sensors to get the pump to start then ensure it stops (and so does the flow of water after the pump stops) with everything filled back up properly again..