I come every couple of years for a conference in downtown SF (Moscone Center) and always stay a whole week (so I can walk around town before/after the conference - usually going north and west towards the shore/golden gate bridge).
I have not throughout the years noticed the supposed infestation of human faeces. I see a lot of homeless people, but not more than, say, Berlin. And I would say the parts of the city I walk through (and especially the parks!) are actually cleaner than Berlin (and Berlin is not that dirty).
Am I just not staying/walking through the really bad parts? Or missing something else? Or does it just take longer exposure to notice?