SalamenceFTW was right, It probably was in fact another Pokemon. Drake from the Hoenn region Elite Four had a Shelgon and a Salamence in his team at the same time in R/S/E. Although that has nothing to do with that. ANY Pokemon can be practically found in the wild in the anime. (Yes, even starters.) So maybe he has two of the Pokemon.
I really do hope this helps and I hope I'm right...First attempt at a real anime question.