To gain better insight into the composition and recycling opportunities of commercial and industrial (C&I) waste, a sensor-based material flow characterization (SBMC) study was conducted at a C&I waste sorting facility. The 2D and 3D fractions from ballistic separation were monitored so that the material composition of both fractions could be determined. While previous studies and studies in the literature have mainly focus on the SBMC results, this paper will highlight the challenges encountered during the measurement that have a potential impact on the results. The focus in this regard will be on non-NIR related challenges, SBMC preparation challenges, and classification challenges.