Occasionally the ender dragon can fly through the end gateways that are generated after the dragon is killed for the first time. When the game realizes that the dragon disappeared is spawns a new dragon. If the player then goes through the gateway the dragon went through the dragon will fly back to the center end island, resulting in two dragons. Additionally if one dragon is killed the portal back to the overworld will open with one dragon still alive. A possible fix may be not allowing dragons to fly through bedrock or making it so they cannot go through gateway blocks