If I had to guess, I would say that the three speeds are having malfunctions as they accumulate mileage. If you think about them these hubs have seen thousands of miles (if not tens of thousands), most of these IGHs are made for recreational usage.(i.e. sub 5k miles) That being said they are also meant to be used by people that somewhat understand how they work, and if not they somewhat baby them. If you get someone with no background with IGHs you could have them twisting and shifting under load causing major wear and tear to the hubs and small parts inside which are a pain to replace. Especially if we are talking about 4-5000 total hubs.

The Nuvinci hubs do not have the steps that a normal hub has. This makes it strange to ride at first, but allows you to have people jump on and move the shifter all they want and cause no damage to the internals. They may cost a little more but in the long run they are more robust and will allow Citibike to not have to replace the small parts inside of the other IGHs. Which will help them to focus on any other issues that may be arising in the bikes.