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, repeatable ad nauseam. Don't really know anything to suggest for that one.