Particularly in the case of tiny bugs on plants, fruits, and vegetables. Why are they not considered batul bshishim since they are obviously not there on purpose (or desirable) and they make up a tiny part of the food.
There is a special rabbinic law which says a בריה, any living thing in it's entirety, cannot become nullified due to it's being special in a sense. You can see more about this in Shulchan Aruch Yoreh Deah siman 100.
In the US, there are acceptable limits to such things as insect parts, rodent hair, and parasites in fish, per FDA regulation. These levels are far below "shishim", but are unavoidable today and are probably far lower today than they were historically. Over six decades ago my (eminent) rabbi (z"l), answered a phone call from a hysterical congregant, who just read that the M&Ms she had bought and consumed contained gelatin and had no hekhsher (to this day I have not checked to see whether M&Ms did then, or do today, contain gelatin, I just rely on his ruling). Now, gelatin is of course animal collagen broken-down by heat, likely from a cow or a pig slaughtered commercially. Rabbi G. assured her that shishim applied, both because of the low levels used and the chemical reduction of the collagen from which it was derived. So she noshed happily ever after. Before synthetic heparin became available, folks got it extracted from some part of a slaughtered pig, likewise some useful medicines from the pituitary gland of a pig. And I know of a fellow whose life was saved by a pig's artery or vein transplanted to his heart (of course, it was not eaten(!!), and I guess medicines are not really "eaten" even if consumed, since they are a pikuakh nefesh necessity). Shishim has always seemed to me a very useful accommodation of halakha to reality.