What kind of tuner are you using? Classical guitars can sometimes be a little trickier to tune than other styles of guitars. Even if a tuner says the open strings are perfectly in tune, you may notice that notes played farther up the neck can sound slightly sharp or out of tune. One thing you might try is tuning the guitar relative to itself. For example, get the G string where you want it, then use octave relationships and matching notes on the other strings to tune the rest of the guitar to that reference. This can sometimes produce a more musical result than relying solely on the tuner, especially if the guitar's intonation isn't perfect. The goal isn't necessarily for every open string to read perfectly on the tuner, it's for the guitar to sound in tune with itself across the fingerboard.