The 3rd fret or some of those in that area might be slightly sharp. Not every fret will be perfectly in tune. The important one is to make sure the 12th fret and the open string are in tune. If the 12th fret is flat, you need to move the saddle forward to shorten the string and raise the pitch. If it is sharp, move it back to lengthen the string and lower the pitch (Pretty sure I got that right, but those directions always confuse me haha). That is what is known as setting the intonation.

The reason you look at the 12th is because it is the octave of the open string. So your 6th string is E open and the 12th fret is also E. You want those 2 pitches to match, but like I said, the other frets won't be perfectly in tune always.

But that doesn't mean that they should be WAY out of tune. If the open and 12th match, but you still have overly sharp notes, take it to a luthier and see what he says. You might have other things to deal with then.