You should read his essay on "Nietzsche, Genealogy, History." https://noehernandezcortez.files.wordpress.com/2011/04/nietzsche-genealogy-history.pdf

In this essay he uses a reading of Nietzsche, specifically his writings on genealogy, to criticize history as it was practiced at least through the middle of the twentieth century. Foucault saw traditional Hegelian history as overly focused on origins and on a totalizing conception of knowledge, as well as teleology.

This is a pretty good synopsis of the main thrust of Foucault's argument. https://lewislevenberg.com/1002

You might also be interested in the Stanford Encyclopedia of Philosophy's entry on Foucault. The SEP (plato.stanford.edu) is a good first-line reference for most major western philosophy. http://plato.stanford.edu/entries/foucault/

Your lecturer may have been referring to Foucault's critique of history as expressed in The Order of Things and The Archeology of Knowledge, according to which the writing of history is subject to epistemological, institutional and discursive conditions of which it is traditionally unaware. By masking the epistemological, institutional, and discursive conditions of its making, history seems to offer transparent access to a past that is in fact a projection of those conditions as they obtain in the present. In this sense Foucault's methodology offers a critique of what your lecturer calls "academic history."