This is fairly common problem with alot of accoustic guitars, the 2nd string when tuned open, is sharp when fretted, some guitars are worse than others but most suffer a bit from this, the main culprit is the uncompensated bridge saddle, I usally fret the 2nd string at the 3rd fret and tune it to the open D, which makes the B a little flat when played open but fairly liveable, or you can make a new bridge saddle, which is pretty easy to do and compensate the B string by moving the contact point for the string back toward the bridge pins, basically just increasing the string length slightly, it may take a little trial and error but it helps............