Focussing Error Issue D90 with Nikon AF 50mm F1.8

You are saying that your camera front-focuses with the 50 1.8, right? In that case, sadly, there is no other solution than to send it in to Nikon for calibration.

D90 has no AF fine tuning feature, unfortunately.

Before sending it in, though, make sure it is not user error. Do some search on google for "front focus" and "AF accuracy testing" or similar topics.