i'm in your conscience
They're probably traded. If the Pokemon are from the same game and it's traded to another game that takes place in the same region, it'll still say "met in ____" as opposed to when traded to a different region, which would say "met in (region)" or "met at a faraway place." For example, if I trade my Altaria from Ruby to Sapphire and we met in the Sky Pillar, when it goes to my Sapphire, it would still say "met in Sky Pillar." So I think it's fine, really, but if it bothers you, just restart it I guess. :/ It seems fine to me, though. They're just traded is all it seems like.
Anyway, I think that answers that, but if you have more questions or my answer doesn't fully convince you (which I mean, don't take my word as law, I was just assessing this with the information I was given!) then feel free to ask more questions in the Q&A thread. It's at the top of this section.
Oh, and it might do you some good to check the trainer card and see the number of link trades the game has performed. If there are less than two, then the previous owner possibly hacked for those.