Make sure the econ button is lit for the auto-stop to kick on when you stop. If it isn't working, then it's something you should bring up with your dealer.

Dealing with a car that's designed with an underpowered gas motor and an underpowered electric motor that works together to get you down the road comes with some penalties that are more pronounced than on a regular car. When you run the AC, it's going to impact milage more than you're used to on a regular car.