Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals widely used for their oil and water-repellent properties. Their environmental persistence and potential health risks have raised significant concerns. As PFAS degrades through remediation or natural processes, they form complex mixtures of the original chemicals, transformation byproducts, and degradation additives. Analyzing PFAS after degradation presents analytical challenges due to possible chemical and physical interactions, including ion pairing, micelle formation, and complexation. These factors can significantly impact the precision and accuracy of PFAS measurements, yet they are often overlooked in PFAS degradation studies. In this work, we demonstrate that with the addition of ppb-level cetyltrimethylammonium bromide (CTAB), a cationic surfactant used in PFAS plasma-based degradation, the PFAS calibration curve linearity, sensitivity, and reproducibility are severely compromised. Isotopically labeled internal standards cannot fully correct these issues. Furthermore, the standard EPA methods 537.1, 533, and 1633 could not accurately recover PFAS concentrations in the PFAS and CTAB mixtures, with severe matrix effects observed for longer-chain and nitrogen-containing PFAS. Among these methods, Method 1633 is currently the most suitable option for postdegradation analysis. Method 1633 showed the lowest CTAB interference because this method used another weak ion pair additive, formic acid or acetic acid (in commercial lab analysis), to acidify the sample before LC-MS/MS analysis and added an isotopically labeled internal standard. For future PFAS degradation studies, we recommend systematically evaluating the matrix effect on the PFAS quantification using a recovery matrix to validate the analytical methods before use.