This can sometimes be the case, but it is rare. At the time of production, there will be a range of acceptable tolerance for the focus set-up of the camera and lenses. In most cases, any slight difference within that scale will be unnoticed, but if the body is at one end of the tolerance scale and the lens at the other, you may find that the two together produce a slight back or front focus; the actual point of focus is slightly behind or in front of the intended subject. Your camera may have an AF Fine-Tune or Micro-adjustment feature that will enable you register the AF position for an individual lens, from which the camera will compensate every time that lens is attached.
It should be noted that this facility should not be necessary for most lenses and is not intended to be a substitute for attention in a service department where fundamental optical problems are concerned.