On every guitar I have owned and currently own, the first couple of frets on the third string can always go slightly sharp....even when the guitar is perfectly intonated.
I've noticed that it is basically attributed to how heavy handed I am when gripping the board and also my finger placement. If I grip too hard, it goes waaaay sharp. Also, the closer I can get my finger to the fret, the better the intonation is.
I've learned to condition my grip and adjust while playing if I need to, both in practice and live performance situations. It hasn't been much of an issue for me once I figured out what was causing it. It drove me nuts until then, though...
Of course, this is just me....your guitar may also be suffering from a setup issue, which any competent guitar tech should be able to remedy. A combination of both heavy grip and a setup issue, that could really take the wind out of the sails.
Either way, I'm sure it'll get sorted out!
Good luck!!!