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"Engine System Malfunction" Warning

I received an "Engine System Malfunction" warning on my 2016 CX-9. The first time I took it to the dealer they told me it was a know TSB issue so they re-flashed the engine management software and it would be fixed. Less than three weeks later, the same thing happened again. This time, the dealer said it was my battery and recommended replacing it "We can't evaluate the engine if the voltages are too low." The battery was replaced and I'm now wondering if the problem has been corrected.

While I don't disagree with the battery diagnosis, I'm wondering if there isn't a specific error code for battery problem, rather than a "Engine System Malfunction." Has anyone else had this problem before?
 
I had the same issue on my 2017 CX-9. I had the software re-flashed and haven't had the warning come up since. It happened about 4 months ago.
 
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2016 Sport @ 2016.5 Sport
My 2018 cx-5 spent a month in the shop after the ESM warning and they said the parts were on national back-order. I was thankful it was under warranty and for 2 different loaners, I just got it back in the last 2 weeks.
 
Did they tell you what
My 2018 cx-5 spent a month in the shop after the ESM warning and they said the parts were on national back-order. I was thankful it was under warranty and for 2 different loaners, I just got it back in the last 2 weeks.
Did they tell you what was wrong?
Mine hasn't had a problem after they replaced the battery so I'm crossing my fingers.
 
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2016 Sport @ 2016.5 Sport
P0126:00 Insufficent coolant temp for stable operation. Coolant control valve assembly not functioning correctly.
 
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