Exchanging the native surface ligands of CdSe nanocrystals with phenyldithiocarbamate molecules is known to red-shift the absorption spectrum and improve the conductivity of nanocrystal films. However, the mechanism of exchange and the details on the interaction between the nanocrystal surface and phenyldithiocarbamates have not been fully resolved. Using NMR and density functional theory calculations, we show that phenyldithiocarbamates decompose during exchange with native ligands. Phenyldithiocarbamate salts decompose when the cation (triethylammonium in this study) acts as an acid, donating a proton to the 3,5-dimethylphenyldithiocarbamate ligand (DMPTC) producing 3,5-dimethylaniline, carbon disulfide, and other decomposition products. While most decomposition products negligibly interact with the nanocrystal surface, 3,5-dimethylaniline chemically binds to the CdSe nanocrystals. This work demonstrates that the ligand exchange between colloidal nanocrystals and phenyldithiocarbamate ligands occurs in a dynamic system with a variety of molecular species.