Stains on stone tools

I was opining that the dark brown color at the tip of Tim MacSweeney's "Quartz Stone" was a stain induced by the use of the stone to pound something. I think staining of stone tools is common and provides some of the most important clues. In some cases it seems as if the hafting material (presumably some kind of leather) somehow catalyzed the deposition of iron. For example here (note brown horizontal stripe):And on the right here:
In other cases the stain seems to soak into the underlying rock, like on the left above or in Tim MacSweeney's stone. I am not sure why it looks "soaked in" except that the stain seems to shade away further from the surface. In the case of the stone on the left in the above photo, I have several other examples of the same material that are uniform grayish beige, without any changes of color.

One more example of surface rust stains:This is a blue mudstone (argillite) axe about 7 inches long. There is a curved brown line cutting off the upper right corner which, I believe, gives me a clue about how it was hafted.

I have a book about someone finding dried blood on clovis points from alaska and then analyzing the shape of the re-crystallized hemoglobin to detect the species of animal the blood came from. They found mastadon blood. It is hard to believe that such materials would stick around so long on the surface of a stone tool but they do.

Update: Another thing I want to point out about Tim's quartz stone is that it is shaped like a hammer with damage from battering on the discolored tip. So it is not just the shading characteristic of the stain but also its consistency with the shape of the item that suggests use stain rather than chemical coloring of the rock.