I was making a test platform to try out some stuff for my future drone carrier. I renamed one of my drones from the default name it was given, to "Drone 2". When I looked at my fleet list, it was still listed under it's old name. But listed under the new name on my navigation menu. The recall to carrier command still worked fine... so I don't think it breaks anything, it's just listed wrong.
I removed the ship from my fleet and re-added it, and it updated the ships name on the fleet menu.