I'm playing through for the first time finally, so I'll prolly have a handful of tile/npc things in a week or two, but for now...
Dunno if it's been reported before (searching "shiny" doesn't yield any applicable results)
Catching a shiny pokemon when paired up with a partner (in this case, Aelita before getting the second badge) does not count toward the "catch shiny pokemon" achievement.
On the subject of achievements, you get a point for "Friendship is magic" every time a pokemon hits 255 friendship, which means you get credited again if that pokemon drops to 254 then goes up to 255