Air-to-fuel ratio (AFR) errors during spark-ignition (SI) engine operation lead to degraded torque tracking performance, increased fuel consumption, and decreased catalyst efficiency. Errors in AFR are commonly sensed using an exhaust gas oxygen sensor and can be caused by a variety of sources. This sensing methodology makes it difficult to distinguish one error source from another. For engine control, it is common practice to assume the error source is in one or two areas regardless of the actual source(s) of error. Identifying the proper AFR error sources is the focus of this research. A disturbance observer is utilised to distinguish errors related to air charge estimation, fuel injection quantity, and exhaust gas recirculation (EGR) simultaneously. This methodology utilises several engine gas-path sensors in combination with a system model to identify error sources. The proposed method is implemented experimentally and demonstrates the ability to properly identify error sources.