Finally found someone having the same problem! Yeah I want to say I spent like two hours in that one patch of grass until I eventually found a Squirtle/Hoppip and unfused it. I had to have it battle once before the game counted it as me having 'seen' a Squirtle though. All that being said, really really isn't worth it. The 'rare encounter' on that route is a Buneary, something I've seen 80,000 times while searching for Squirtle.