While a majority of system vulnerabilities such as performance losses and accidents are attributed to human errors, a closer inspection would reveal that often times the accumulation of unforeseen events that include both component failures and human errors contribute to such system failures. Human Error and Functional Failure Reasoning (HEFFR) is a framework to identify potential human errors, functional failures, and their propagation paths early in design so that systems can be designed to be less prone to vulnerabilities. In this paper, the application of HEFFR within the complex engineering system domain is demonstrated through the modeling of the Air France 447 crash. Then, the failure prediction algorithm is validated by comparing the outputs from HEFFR and what happened in the actual crash. Also, two additional fault scenarios are executed within HEFFR and in a commercially available flight simulator separately, and the outcomes are compared as a supplementary validation.