Well if it's an acoustic, it's more complicated if it's an intonation issue. You are kind of stuck to a certain extent. On electrics, you can adjust the saddle back and forth easily. Acoustics don't have the same set-up so you don't have a saddle that you can move to adjust each string.

I would take it in to a shop and ask them to have a look at it.

$200 is fine for a beginner guitar. I wouldn't even really consider it a "cheap" beginner guitar. Paying like $50-100 would be cheap and would almost guarantee that there are going to be huge differences in playing.