At the end of the day, a villain is a villain, and for them to end up turning on those who claim to share that title maybe shouldn't be as surprising as it often is.
Most of the time, obviously, it's you, the player, that they're really after, and they're not about to let anyone else get in the way of their goals, whatever that entails. On the flip side, sometimes it's you that's poked your nose where it shouldn't be; a place where the bosses have bigger axes to grind with each other than with you.
Whether it's satisfying or anticlimactic watching a heavily built-up foe snuffed out by someone other than yourself, it's almost always totally unexpected, and why we tend to assume that villains have some sort of universal code of honour is anyone's guess. Because in reality, they don't - and where they're concerned, the enemies of their enemy are certainly not their friends.
Now that bosses are killing other bosses, will video game heroes soon be out of a job?