[arfman2882]

Intonation will never be perfect on an acoustic guitar. It is possible, though, that you are fretting too aggressively and bending the notes out of tune.

My recommendation is you take it to your local tech and have them look the guitar over. Sometimes the top warps behind the bridge. A more likely scenario is that your relief will need to be adjusted or you’re fretting too aggressively. Go get it setup professionally and then make sure to get a setup about once a year and try to keep your guitar comfy while it’s at home.