Classical interpretation of drilling mud-gas molecular and isotopic data in petroleum systems can be impacted by both natural and engineering processes, which can introduce allochthonous and/or isotopically unrepresentative gas species. This study investigates (1) widespread primary biogenic methane (C₁) and its impact on mud-gas–based petroleum system interpretation and on the properties of the petroleum fluids in the subsurface, (2) differentiation of migration-mixing versus diffusion-leakage in petroleum systems, and (3) bias introduced by gases generated at the drill bit, including alkenes and isotopically changed gaseous alkanes. Our goal was to provide solutions to flag impacted intervals by the above processes, minimize resulting interpretative-bias, and extract additional information about the fluid using advanced mud-gas logging (AMGL) tools and workflows. An AMGL interpretative methodology was developed using a combination of logs of C₁ to pentane (C₅) concentrations and δ¹³C-C₁. This approach allows identification of subsurface intervals containing nearly pure background primary biogenic C₁ and can quantify its concentration per rock volume. Consequently, thermogenic end member fluid types can be differentiated from mixtures with the biogenic C₁ and assess its impact on the gas–oil ratio of the mixture. Additionally, two different processes can be responsible for mixing trends apparent on classical interpretation charts (e.g., modified Schoell diagram). The presented analysis of AMGL allows the deciphering of migration-mixing versus diffusion-leakage mixing trends using studied wells as examples. Another bias of mud-gas–based interpretation originates from artificial gases generated by drill-bit metamorphism (DBM). Evidence that DBM produced artificial alkanes in addition to alkenes via cracking of oil-based drilling mud included strong correlation of concentrations among alkenes. Furthermore, the concentration of alkenes strongly correlated with the magnitude of shift in δ¹³C of C₁ and ethane (C₂) between mud-gas and solution gas from bottomhole fluids sampled at equivalent depths. The artificial alkanes, contributed by the drilling process, can strongly bias and interfere with petroleum systems early interpretation based on mud-gas molecular and isotopic ratios. The bias depends on relative contributions of petroleum reservoir-liberated mud-gases and DBM-gases, which in this study reached half of the total C₁ and C₂ in the analyzed mud-gas. Conversely, alkene concentrations can be used as mud-gas quality check parameters and early indicators of excess heat generated at the drill bit.