Molecular Quantum Dot Cellular Automata (mQCA) are among the most promising emerging technologies for the expected theoretical operating frequencies (THz), the high device densities and the non-cryogenic working temperature. In this paper, we performed an analysis of the possible fabrication defects of a molecular QCA wire built with ad-hoc synthesized bis-ferrocene molecules. We then evaluated the fault tolerance of a real QCA device and assessed its performance in non-ideal conditions, by defining a new methodology for the fault analysis in the mQCA technolog