1- Once you open the lower 2 floodgates, fly to the far right. There will be a platform you can reach now. Climb up the vines and I'm pretty sure it leads to a chest

2- After entering the dam and using the elevator, you get in a fight, the chest appears afterward (I'm guessing you got that one)

I'll go look around there again.

1-When you fly past the bridge thing that goes to the Elite enemy, hang a left before you get to the plateau that has/had a big crystal and the big enemy. You should end up near another plateau, closer to the lava, with lots of enemies. Defeat them all and chest appears.

2- The area where you push over the rock to climb the wall- Turn around at that point, and go back towards the beginning of the level, before you leave that big area, you'll see a small cave to the...left I think? It's got enemies and a dark crystal inside (it's part of the cave wall, look around until you see your energy dropping). Smash the crystal, and part of the wall gives to show a chest.