I had similar issues when I moved to the D7000. So I simply removed possile causes -
Use spot metering Set - autofocus mode to AF-S - AF-Are Mode select Single point AF - Set the center focusing point and lock the control - a2 to Focus - a3 - Off - b4 - 6mm - f4 - None (just use the shutter button) - Turn on beep (d1)
try these settings with a couple of lenses
If your photos are regularly focused on the wrong area - then it is time to take a real good look at the camera
If your shots are cosnistently coming out focused as desired - then you have invested time correlating how this camera's focus and metering sytem works within your expectations. Start changing things like AF-S to AF-C 9 points, then change the metering to spot and matrix, etc.