You can't normally get Squirtle in Pokemon Ruby. If you used a game hacking device to obtain one, maybe Pokemon Emerald was able to detect that?
Emerald also refuses trades until you've obtained the Running Shoes, though that happens so early in the game it's probably not what's wrong in this case.
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Yes, you can get a Squirtle in Pokemon Sapphire. However, it cannot be caught in the game. It must be traded from FireRed or LeafGreen (or Emerald) and will even register on your Pokedex after you defeat the Pokemon League. Keep in mind that Pokemon like Blastoise or Wartortle can breed to produce a Squirtle.
The Growlithe cannot be found in Pokemon Emerald but you can trade it fromPokemonFirered.growlithe cannot be caught in emerald, Sapphire or ruby. it must be traded from fire red
Squirtle is not available in Pokemon Crystal. Squirtle can only be found in Pokemon Red, Blue, or Yellow. Squirtle can be traded to Crystal from those titles.
Shaymin was only introduced in the 4th generation games (diamond, pearl, and platinum) and cannot be found or traded to Pokemon emerald.
You can't.Burmy is a generation 4 pokemon, it did not exist in games before Diamond and Pearl. It cannot be caught in earlier versions such as Emerald, even if you use a cheat device.It cannot be traded to Emerald from the 4th generation games- trading from D/P to Emerald is impossible.Therefore, it is impossible to obtain a Burmy in Pokemon Emerald.