went to try and flush the tanks of my 2020 3721 RL just to try the system. When I hooked up the hose and turned it on the storage compartment started to fill up with water. After inspection behind the panel found that the connection went no where. No hose connected to it. Was i supposed to switch a line back there or was it a defect from the factory. ?
That's a defect. The black tank flush line connects directly to the black tank through an anti-siphon valve. It should have been caught by the dealer at the pre-delivery inspection, but frequently that doesn't happen.
Most RVs use the San-T-con system or something similar. As has been already noted, the connection you were using should go to an anti-siphon valve and then to a spray nozzle inserted in the top of the black tank. The only water you should ever see is the small amount in the hose from the connection to the anti-siphon valve that will come back out when you disconnect. And that's all clean water, so it isn't a concern.
