The functionalization of nanomaterials has long been studied as a way to manipulate and tailor their properties to a desired application. Of the various methods available, the Billups–Birch reduction has become an important and widely used reaction for the functionalization of carbon nanotubes (CNTs) and, more recently, boron nitride nanotubes. However, an easily overlooked source of error when using highly reductive conditions is the utilization of poly(tetrafluoroethylene) (PTFE) stir bars. In this work, we studied the effects of using this kind of stir bar versus using a glass stir bar by measuring the resulting degree of functionalization with 1-bromododecane. Thermogravimetric analysis studies alone could deceive one into thinking that reactions stirred with PTFE stir bars are highly functionalized; however, the utilization of spectroscopic techniques, such as Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy, tells otherwise. Furthermore, in the case of CNTs, we determined that using Raman spectroscopy alone for analysis is not sufficient to demonstrate successful chemical modification.