Tuning each open string perfectly doesn't guarantee that fretted chords are in tune. The fingers, the frets and the strings all play a part.
Common causes:
- Heavy fretting: pressing hard pushes notes sharp. In a chord, a few sharp notes clash.
- Sideways pull: fingers that push strings toward the floor or ceiling bend them slightly.
- Intonation: if saddles are off, fretted notes drift more the higher you go.
- Old strings: worn strings go out of tune unevenly along their length.
- The tuning system: frets divide the octave into equal steps, a compromise that makes some intervals slightly wide or narrow. Major thirds, like the B string in a G chord or the G string in an E chord, are where you hear it most.
How to improve it:
- Fit fresh strings and check intonation.
- Fret lightly, right behind the fret, with fingertips pointing straight down.
- Tune with a clip-on tuner every time you play.
- If one chord you play often sounds rough, tune slightly while holding it and see if the result suits your songs.
A guitar that still sounds rough after these steps may have a high nut, which pulls the first few frets sharp. A technician can check it.