Seems to be that Foucault has very negative views about the idea of some type of innate means of organization - Chomsky mentions such means to account for how a child will at least have the ability to identify a language as something which can be used; the mere existence of language around the child would not be able to lure the child if such an innate ability was not there.
Foucault, around the mark of the half hour, even says that in his view it isn't evident why one would have to look for such abilities in the mind, instead of looking for them in various external (physical or social) structures.
This does strike me as odd, since I was under the impression that the debate about covert relation of empirical data to innate procedures (without which they wouldn't be picked up, and furthermore they are being fused with innate data while picked up) was pretty much over. No need to resurrect Hume or the empiricism vs idealism argument.
After that - at least what is shown in the video - the discussion is about the idea of justice and whether it is innate (not dependent on social reality, such as existence of classes) or itself only a product of the social reality. Here, again, Chomsky takes the first position and Foucault the second one. But imo Foucault's position is untenable since even if social reality would change and become class-less, the residue of the idea of injustice would not perish, since no idea does, and therefore the idea itself would not require empirical data to maintain it (despite, arguably, not being as easy to trigger as with things as they now stand).
There is a simpler way to present this, and ultimately it goes down to a comment on what Plato said (having Socrates say it), that people are unjust because they do not know their own good; the success of a will to power can seem very good for oneself as long as they maintain some relevant class of vigor needed to perpetuate the inherently unstable system of a power-trip - but not longer than that.