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I believe the incidents I was referring to specifically happened on the route leading from Pewter to Mt Moon, seeing a kid I couldn't avoid spawned in while I was heading back to avoid battles between me and the center before entering, then the one that replaced a trainer I'd just fought was...
Love the game and story so far, really an interesting way of remaking things.
Have noticed a few minor bugs though, mainly that Pluck doesn't do its effect at all having seen multiple pokemon chow down on a berry right after it being used on them. Also at least one mon has its TM learn set...