It's probably a glitch. I've seen a lot of glitchy stuff in these fights, especially where the environment is involved. It is already common knowledge that your exact 'position' will not appear the same on every person's screen, so when you are standing in the right spot between lava, you may still get hit... and when you are standing directly behind a rock on garuda, you may still get hit. It's unfair, but it's a glitch because of this. Yoshi P also mentioned this issue with his plans to fix it.

As far as Hellfire doing so much damage... How soon did you kill the nails before he went to the center to Hellfire? If you kill the nails RIGHT before he Hellfires, they may still be counted as part of his Hellfire because they didn't completely register as dead/gone. As others have said, sentinel is a very helpful ability. Be sure to use it IMMEDIATELY when you see him jump to go to the center. If you use it as he's using his ability, it may be too late.