Many years ago I took apart a Nikkor 50mm 1.4 non-AI lens to clean it, and if my memory serves me well, there was a stop built-in to the lens so that the focus ring stopped at infinity. Perhaps the AI version is similar, and the stop is chipped or bent so that the focus ring goes too far.
The infinity stop on all of the manual focus ai or ais lenses I have is built in to the lens, so unless the rear element hits something as it recedes to the infinity position, there should not be an issue with the body. If the rear element hits something, the focus ring will not go far enough to reach the infinity setting, so this does not apply to you, as your lens goes too far.
By the way, my 300-mm 2.8 AIS ED goes about 7 mm past infinity and this is normal, to allow for thermal expansion (it is internal focus, and 7 mm is not that much compared to how far the focus ring turns for the full-focus range).