I am yet another rider with the Check Engine Light on, and it's been on for 6 weeks now. I did some research, and some of this is repeats of other posts in this string, but I've got time on my hands, so...:
I called Yamaha Central in California. Spoke to a person in the 'technical' area. Yes, there is a problem, and they know about it. There are a couple of silly ways the CEL can come on: Key not being in just right and start, sidestand down and kill switch used, etc. Yamaha Japan is working on a software fix, and it has not happened yet. There will be a recall notice... eventually.
However, (and he was adamant) this is a warranty service issue. If the light comes on and there really isn't anything wrong - meaning, there really is no reason to 'check engine' - then any Yamaha service department can and should clear this for you. Under warranty. Free of charge. If there are any questions about this: Call Raymond. 800 962 7926 x17442.
I also spoke with a Yamaha shop and service rep I trust, at D & H in Cullman, AL, where I bought my '16. They tell me that there is a way to clear this check engine light, and it can be done at home. But... it has to do with holding your tongue in the left cheek, crossing your eyes, and pushing a number of buttons on the console is just exactly the right sequence. This next is strange, but I'm telling what I heard. IF they had had a '16 in the shop when I called, they would have gone over the sequence with me. But they didn't have one. It seems that, if they know the sequence, they could tell me.
I was told, it is a very careful sequence, and, if you do something wrong at one step you get into the ABS programming instead of the Check Engine, and you can really mess things up. However, and again, adamant: you do NOT have to have wires and connections and gas tank removals to do this: it can be done on the bike console.
Now...can one of you other guys that has a reputable dealership you have a good rapport with...find the 'careful sequence', and post pics of each step? You would have legions of adoring fans, I am sure!