Its very possible that I may just have miscounted or forgotten to count some.
Today's update, updated the counter to 92 since I forgot to count one on the western plains but that still would leave 7 more than I counted.
You can can check each area with the scan ability, if you have more flames in that area than there should be.
Also one thing I don't know/tested is, if flames and chest respawn then changing to a new version, if taht is the case it certainly could explain taht but sicne you mentioned no duplicates I guess I just forgot to count some.