So I'm on the last level of Rayman 2 (The Crow's Nest), and whenever I get to the part where the lava raises, the robot clips through the ceiling, meaning that I can't shoot it's arms to make it fall. Any help?

Has this happened multiple times, or just the once?

I had this happen to me a few times. What I ended up doing is using the secret to get unlimited ammo and fighting him that way. To get unlimited ammo, you first pick up the regular ammo. Then, hold down jump and shoot and fly to the topmost point of the stage and you'll go through a secret tunnel. after dodging obstacles there is a blue glowy that will teleport you back to the fight with unlimited ammo. This way I was able to fight him without triggering the rising lava which is when he would clip for me.

I don't recommend cheating, try reinstalling the game(Backup your saves, though). Let me know the results.

I tried reinstalling, same thing happened.

Hmm... Odd... Okay, what's your PC's setup? (OS(Specify if 64- or 32-bit), GPU, CPU, RAM size, etc.)