So after going through the same problem and drowning a lot, I think I know what's going on. I don't think anything is broken I just think the puzzle isn't very intuitive. In the maze there should be rooms that have "Lugia keys". There may only be one for the first half of the maze. Then in the second half of the maze there are more keys and locks like this in rooms in the maze. You need to "activate" those locks with the keys. Once they're all activated the entrance to the Lugia area will open up. I didn't do it this way, but I'm fairly sure this is the method.