It happens in a lot of boss fights. It's the same reason sometimes there are still minions wandering around after a fight when you killed the boss already. Sometimes you have the good/bad luck to start against only minions. Good because you get to fight the boss without his minions. Bad because you have to fight 2 battles. These things usually happen when people port into dungeons, or someone has left the dungeon or is in another part. The game thinks 3-4 people are in the dungeon, but only 2 join the battle, so it starts with 3 enemies, sometimes the boss isn't one of them. Not really a glitch.