The dark matter hit every one in the city, but only a few became metahumans because of it.

You didn't pay attention to the scene I think mate, Joe didn't say he was affected by the dark matter but that he, iris and entire town got hit by it when the particle accelerator blew, which it did in the pilot, he was making a point how an entire city got nailed by dark matter but only a handful of people were affected by it.
Though I wouldn't have been shocked had they made such a silly cock up by having him say such a thing which wouldn't make sense, but then again neither does the shows "rules" on time travel.