I have a similar experience with Quake's final boss. It's the only thing in the entire game you don't kill by shooting. Took me 3 freaking days to figure it out.

It's stupid as hell because it's like the easiest thing to do, but no game had anything remotely like that, and it wasn't a mechanic shown to the player at all in SP (if you don't know you have to telefrag the boss by jumping into a gate when a purple spikey thing flying around the room clips through the boss).