2013~2016 Key left in vehicle warning beep

2015 CX-5. Stuck bag with keys into luggage area. Closed the lift gate. There's used to be a warning beep when I did this, but now it just locks. Any ideas?
 
Does the 2015 have push-button start? If so maybe the fob battery was low and didn't broadcast signal far enough for car to detect key was still in the vehicle. Maybe there was stuff in the bag blocking the signal.
 
Does the 2015 have push-button start? If so maybe the fob battery was low and didn't broadcast signal far enough for car to detect key was still in the vehicle. Maybe there was stuff in the bag blocking the signal.
No battery is fine, and I checked with the other fob. One other thing, the external handle lock buttons are flakey, I think that might be related.
 

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