recent advances enabling multiqubit designs that exhibit coherence lifetimes on the order of hundreds of μs, material quality and interfacial structures continue to curb device performance. When niobium is deployed as the superconducting material, two-level system defects in the thin film and adjacent dielectric regions introduce stochastic noise and dissipate electromagnetic energy at the cryogenic operating temperatures. In this study, we utilize time-of-flight secondary ion mass spectrometry (TOF-SIMS) to understand the role specific fabrication procedures play in introducing such dissipation mechanisms in these complex systems. We interrogated Nb thin films and transmon qubit structures fabricated by Rigetti Computing and at the National Institute of Standards and Technology through slight variations in the processing and vacuum conditions. We find that when Nb film is sputtered onto the Si substrate, oxide and silicide regions are generated at various interfaces. We also observe that impurity species such as niobium hydrides and carbides are incorporated within the niobium layer during the subsequent lithographic patterning steps. The formation of these resistive compounds likely impact the superconducting properties of the Nb thin film. Additionally, we observe the presence of halogen species distributed throughout the patterned thin films. We conclude by hypothesizing the source of such impurities in these structures in an effort to intelligently fabricate superconducting qubits and extend coherence times moving forward.