I put my car in neutral, and the rpms went up and down and then my check engine came on. I turned my car off and it was fine after that. what happened?

Not for sure, as it could of been many things adjusting but if engine light ever comes on have it scanned and the one thing I can not say enough is be sure your timing belt is within the owners manual specs on age and mileage and if it is time to install a new belt do so. Do a tune up too, Distributor cap, rotor, spark plug wires, spark plugs, PCV, air filter, ect., check for vacuum leaks, And that all sensor connections are clean & tight. I have seen one Honda that in neutral its rpm's were up & down up & down the whole time about 1000 rpm's or just less and when putting the new timing belt on the timing marks were one mark off indicating the old belt was stretched. The new belt and putting it back in time solved this issue.I had to back the head up one notch, I would check it just to be sure.