Manual control of switch doesn't work after SmartApp runs

I have a GE Smart Dimmer, Z-Wave, In-Wall, 12724 set up in a 3-way configuration to control outside lights.

If I use the SmartThings iOS app or Amazon Echo to turn the lights on or off everything works fine and I can then use the wall switch manually to turn on or off as well.

I have the Smart Lighting SmartApp set up to turn the outside lights on when my phone has been away and presence is then detected between sunset and sunrise. This works great as well.

The problem is that after the lights turn on due to Smart Lighting running, I lose manual control from the switch. Trying to turn the switch off will not affect the lights, and I have to use the App or Alexa to turn the lights off. Is there something in the SmartApp that prevents manual control? This is affecting the WAF.