Now I see why Wells has such a large leap. It must help him jump to conclusions =P
Lugia might be ocean themed, but it isn't a water type. It's Psychic/Flying. Plus, his outfit is totally wrong for Kyogre. Colours flipped the wrong way, too much white not enough blue.
I'd like to raise the point that I'm fairly god damn sure that Rayquaza would be able to differentiate Kyogre and Lugia with incredible ease; as he does serve as the peace keeper between Kyogre and Groudon; and can sense when they get out of hand - so yeah, I'm confused on this move as well.