Octane ratings are not something for which a fuel delivery system is tuned, as they don't affect the air/fuel ratio. Switching between 87 and 93 octane pump gas in any stock production vehicle that's designed for 87 octane should be completely seamless. If anything, the higher octane might allow the knock sensor some time off and let the ignition run slightly more advanced, thus improving throttle response. Also, the additive packages in the 93 octane fuels may also yield slightly higher energy densities in the fuel, allowing slightly higher output and better fuel economy.
I'm not sure which brand of fuel you were using, and what the condition of the fuel itself was, but if the fuel was stale, or if its physical and chemical properties differed significantly from pump gas, then I can understand how you would have problems. However, if the fuel was fresh and it was something like VP Performance Unleaded or 76 Unleaded Racing Fuel which are both oxygenated, 100 octane, unleaded fuels, then I would be surprised that your bike noticed a difference.