What kind of fuel should I use?
The owner's manual specifies 87 octane unleaded gasoline.
Having too high an octane is never harmful, but having too low can be harmful. That said, there's still no point in using an octane higher than what the factory says unless the engine's knocking. With an older engine, sometimes you get knocking unless you go with a higher octane. You're not going to get a performance gain with a higher octane fuel.
(which is the only difference between the cheap gas and the expensive gas at a station) is a combustion inhibitor. It does not make gasoline burn better in any way, it actually prevents the gas from burning too soon. This is very useful in a high-compression, high-performance engine like those found in sports cars and high-performance motorcycles. That's why it's recommended for those engines. However, for the Ninja 250, having combustion of the gasoline inhibited will result in an incomplete burn. This, in turn, leads to raw, unburned fuel going out with the exhaust, which reduces fuel economy, reduces performance, and increases pollution. It won't hurt anything, but you're throwing away your money by buying a higher octane fuel than you need.
At higher elevations, octane numbers will be different to compensate for the different combustion conditions. You should be able to use the lowest-octane gas sold in the Ninja 250 in these situations, but if you experience any knocking or unusual noises from the engine, switch to a higher octane fuel.