You ever eat a sausage? The casing is made out of intestine. Before it was used as a sausage casing, it was used as a shit container, and it probably still contains traces of shit.
It also probably contains a few radioactive atoms, a bit of mercury here and there, maybe some arsenic…
Until and unless food is synthesized from atoms by a Star Trek replicator, it’s going to contain things you don’t want to eat. The best we can do is remove most of those things, but try as we might, we can’t remove them all.