In 1991, the Ohio State University investigatory panel found that Paquette had plagiarized a NSF proposal, that he was also a reviewer for, and included sections in a paper he published in the Journal of the American Chemical Society. The NSF's Office of Inspector General (OIG) found that Paquette knowingly "submitted falsified evidence for the purpose of disproving the misconduct in science charge" and made "false statements under oath in the OIG investigation concerning the authenticity of the evidence". The falsified evidence consisted of a computer disk that included a "'mock draft,' a copy of the paper's final draft that Paquette had marked up to look like an earlier draft" and was back-dated prior to Paquette's review of the NSF proposal and, importantly, prior to the manufacture of the disk. The US Secret Service also found that someone had attempted to erase the lot number of the disk. In 1998, the NSF entered into a binding settlement with Paquette: Paquette would voluntarily exclude himself from any federal funding for two years and the NSF would not "issue a finding of misconduct in science".[5][6][7]
Paquette's honors include Sloan Fellow, Guggenheim Fellow, ACS Award for Creative Work in Synthetic Organic Chemistry, and the Arthur C. Cope Scholar Award of the ACS.