Generally speaking, many charge controllers have fans. Those that do not use a heat sync of some type. Our charge controller fans (off grid application, not in our Class B) often come on and cycle off. If it has a fan and comes on and cycles off I sure wouldn’t worry about it, however, hopefully someone with your charge controller can give you more specific feedback.
2016 (Mercedes) PW Ascent > 2018 (RAM) WGO Travato ‘K’