I have the Core Set and AoU expansion and I love the game so far. I think I know the answer to this question but is there a way to buy the cards that I don't have 3 copies of without having to buy 2 more copies of the CS and AoU?

There are a few places out there that sell single copies of cards, including a certain auction site that I probably shouldn't mention, but they're generally overpriced to the extent that if you want to get anything approaching a full playset it's going to be considerably cheaper to just buy the extra sets.

Basically, if you just want a handful of extra cards then it may be worth shopping around but any more than that and it's a waste of money.

Either way, there's no way to buy single cards except by buying them off someone who's broken a set down.