We study fractional Skyrmions in a $mathbb{C}P^2$ baby Skyrme model with a generalization of the easy-plane potential. By numerical methods, we find stable, metastable, and unstable solutions taking the shapes of molecules. Various solutions possess discrete symmetries, and the origin of those symmetries are traced back to congruencies of the fields in homogeneous coordinates on $mathbb{C}P^2$.