Rancourt is widely known for his confrontations with his former employer, the University of Ottawa, over issues involving his grade inflation and "academic squatting", the act of arbitrarily changing the topic of a course without departmental permission.

[3] His conflicts with the university started in 2005 when, in what was termed "academic squatting", he changed a course to focus "not just [on] how science impacts everyday life, but how it relates to greater power structures".

[4][5][6] In June 2008 a labour law arbitrator sided with Rancourt and ruled that "teaching science through social activism is protected by academic freedom".

[6] Rancourt was removed from all teaching duties in the fall of 2008 because the dean of the faculty of science did not agree with his granting A+ grades to 23 students in one course of the winter 2008 semester.

[22] In June 2011 University of Ottawa law professor Joanne St. Lewis sued Rancourt for $1 million over two U of O Watch blog posts about her, including one which called her a "house negro".