I bought a 2018 CX-5 Grand Touring about a month ago. It only came with 1 key FOB. So I purchased one through Amazon and its a "wiped" OEM FOB. All S/N numbers, model numbers are the same as the FOB I have. I had a locksmith program it. It works to unlock / lock all doors and open and close the hatch and start the car. But now I have a "Keyless System Malfunction" along with a icon of a yellow key and an exclamation (!) point. I have disconnected the negative side of the car battery and left it disconnected for about 60 minutes. I have checked both of the batteries in each FOB and they are both new and at 3.0v. Now one thing the locksmith mentioned is that all cars are registered with 2 keys brand new, since this car is missing 1 key and I had another one programmed for the car, he told me that the on board computer is now showing 3 keys registered to the car. And that he couldn't delete the "lost" key.
All I want is for the "System" error to go away. Any help will be appreciated.

 

Take it to Mazda.

 

I figured as much. If you don't mind me asking, is it because the on board computer is recognizing 3 key FOBs? And the locksmith should've deleted the "missing" one? Just doesn't make any other sense to me cause the FOB is working just fine. And I could at least try and get some of my money back from him.

 

Without scanning for fault codes its a weird situation. Anytime we add a new key using Mazda's software any old keys/fobs/remotes not present at time of programming are automatically deleted from the system.

 

We have the two fobs we bought originally with our 2014 Mazda 3. One had a dead battery for quite a while, just replaced; one works just fine. Bad fob exhibits usual "recovery" behavior: will start car by being <2" from Start button when Start is pressed (near field chip is working?), but none of the fob buttons work (radio needs reprogramming?). I have seen instructions on how to reprogram a key fob that gets inserted, but what about instructions for reprogramming these, that are just keyless push start fobs? Surely it's just hold down some combination of buttons while rubbing my tummy and patting my head ...