Orphans of the Sky by Robert A. Heinlein

And he learned the true nature of the Ship and its mission between the stars. Then Hugh was captured by the muties and met their leader (or leaders), Joe-Jim, with two heads on one body. The current situation is a bifurcated population of the original crew and 'muties' who are physically deformed existing in different parts of the ship.

The tale opens with a generation ship that has experienced a past traumatic event.

Were they evil incarnate, or merely a divine check on the population, keeping humanity from expanding past the capacity of the Ship to support? Orphans of the Sky is a novella by Robert A Heinlein. Of course, there were the muties, grotesquely deformed parodies of humans, who lurked in the upper reaches of the Ship where gravity was weaker. Indeed, how could the Ship move, since its miles and miles of metal corridors were all there was of creation? Science knew that the Ship was all the Universe, and as long as the sacred Convertor was fed, the lights would continue to glow and the air would flow, and the Creator's Plan would be fulfilled. But he also understood this was actually allegory for a voyage to spiritual perfection. Hugh had been taught that, according to the ancient sacred writings, the Ship was on a voyage to faraway Centaurus. His worldwide bestsellers have been translated into 22 languages and include Stranger in a Strange Land, Starship Troopers, Time Enough for Love, and The Moon Is a Harsh Mistress. A fix-up consisting of the novelette Universe (1941) and the novella Common Sense (1941). Heinlein, four-time winner of the Hugo Award and recipient of three Retro Hugos, received the first Grand Master Nebula Award for lifetime achievement.

Orphans of the Sky by Robert A. Heinlein