I know there's a few boss battles I've spent several hours on if difficult and long, die and have to start over. Don't know the exact times and it's been a while.
I know I had a lot of difficulty off the top with Riku in Kingdom Hearts: Chain of Memories after Destiny Island (the original Gameboy Advance one) when I was younger, I had a lot of difficulty with the final boss of Silent Hill 3 on Hard combat difficulty with how I played on my first playthrough (had a lot of ammo, almost no healing items). There's definitely more though, and some I have spent more time on, but I'd need to see the game to remember.