[Yakaru]

Two thoughts on this:

It could be the suspension. The stock Ninjette suspension is not the best even when tuned and if not appropriately set this could easily make the ride feel bumpier/less stable

It could also be the advantage of the Ninjette: light weight/flickability. A larger bike will weigh more and thus have more momentum keeping it going the way it's going. It will also have wider tires for reasons already discussed. If you're tight on the bars or otherwise giving input in rough situations then this ease of maneuver could work to your detriment and make the bike feel less stable. Good throttle control and light on the bars is the number one way to stabilize a bike, regardless of size.