Not all gentsuki are 50cc bikes. There are 100cc, 125cc, etc etc. On the smaller ones, such as the 100cc, it is hard to tell them apart from the 50cc just by a glance.
At any rate, the majority of times I have seen gentsuki pulled over (and I have seen it a lot) was for being in places they weren't supposed to be. A favorite tactic of Tokyo traffic cops is to wait on the far side of an overpass and catch 1) cars for seatbelt violations and 2) 50cc scooters for being on the overpass, if it happens to be one they are forbidden from using.
That, and the weird thing about the right turn at some intersections.