What kind of fuel should my 2006 Honda civic get?

I just recently got the car. The car that I owned before was an older '97 model and I was used to getting regular(87 octane) gas for it. With this car, I got it from a used dealer/car shop and the car had little gas in it. So when I purchased the car, I had to go straight to the gas station to fill it up and I used the regular grade. The car was fine that day, but the next morning the check engine light came on. Everything was inespected, or so I've been told, from the oil being changed, brakes, transmission etc. I recently went back to the dealer so they could check the engine to see what was causing the light to be on. After the mechanic did his thing, he asked me what kind of grade of gas I was using and I told him regular which he then told me that that was the cause of the light being on and that I should use plus (89 octane) instead since its a newer model car. However, in the manual it said to use grade 87 OR UP. So basically should I listen to the manual or the mechanic? And while I'm waiting for my gas to deplete so that I can use the next grade, could anything acutely serious happen to my engine or am I fine for now and just use the next grade higher next time?

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