It's a tough choice, but if I had to choose it would be Betrayers of the Truth by William J. Broad and Nicholas Wade. The book deals with the problematic ways fraud is dealt with in the scientific community, namely as an exceptional phenomenon, a bad-apple type of analysis that unwittingly brushes off the structural issues of academia.

A honourable mention would be Silencing the Past by Michel-Rolph Trouillot which questions the layered process of producing history. The production of history is itself a product of history that should not be taken for granted. All of this is showcased through a quick overview of Haitian history.