If what you're saying is the fretted note is slightly sharp, then you're probably just using too much pressure on the string, especially if you have large, (jumbo type) frets and/or a high action. Try using just enough pressure to cleanly fret the note and no more. Experiment, you don't want to be pressing harder than you need to anyway. As Kirk said, tuning a stringed instrument is always some sort of compromise.
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