Yeah, I saw Lugia too! 0_0
But you CAN get Lugia later on, but it's post-game and pretty complex...
R-301 Lugia Location: Offshore Mironda Island - The Union
The next main ranger sign you'll get is for the legendary bird, Lugia.
To get it, you need to get all 300 Pokémon in your Ranger Browser and
head to Rand's House to get a mission. Follow the mission to the
Undersea Cavern where you confront Blue Eye. Follow her out of the
cave and Lugia will attack. Catch it and you'll get its sign. This
Ranger sign allows you to rechallenge Lugia at any time.