Van Breda Kolff's tenure at St. Bonaventure ended abruptly in controversy late in the 2002-03 season. St. Bonaventure admitted junior college transfer Jamil Terrell with only a welding certificate in lieu of necessary academic credentials. Athletic director Gothard Lane had told school president Robert Wickenheiser in no uncertain terms that Terrell was ineligible. However, Wickenheiser, under prodding from his son Kort, who was also one of Van Breda Kolff's assistants, unilaterally declared Terrell eligible. School officials didn't seek guidance from the NCAA about Terrell's eligibility until the 2002-03 season was nearly over. The Bonnies were forced to forfeit every game in which Terrell played, and were also barred from the Atlantic 10 Conference tournament. In protest, the Bonnies players opted to sit out the last two games. Van Breda Kolff denied knowing about the scandal, and was cleared of wrongdoing.
On April 25, 2007, he was named as one of three finalists to become the new head coach of UC Riverside's men's basketball program.