Complexities arising from interaction between multiple inter-connected components in an autonomous cyber physical system can potentially result in differences in intended and observed operations of a CPS. To perform fault analysis of a CPS it is imperative to explain this discrepancy in terms of the components of CPS control code. A system estimates a “mined” hybrid system representation of a CPS based on observed input/output traces and extracts a state machine representation of the CPS control code. The system compares the “mined” hybrid system representation with the extracted state machine representation simplification of the CPS code to identify discrepancies between expected and observed operation of the CPS. The system explains discrepancies in terms of call conditions as binary or unary operations on input and output variables and status of function call arguments.