Most modern lens designs use special low dispersion elements, like ED glass, which has some small variance in its optical abilities that varies with temperature. Put simply, the "infinity" position changes on these lenses at different temperatures. The autofocus system, of course, doesn't go by the markings on the focus distance ring, it works by phase or contrast detection. Likewise, if you manually focus such lenses visually, you're fine, too. But the focus distance markings are not perfectly reliable, and that's one reason why we see camera makers moving away from providing them.
Another reason why you often find the telephoto lenses focusing past infinity is the potential use of teleconverters. Having an extra mount in the optical path means that tolerances can slip just enough that actual infinity couldn’t be attained with a teleconverter in place.