Maybe they made a hardware/software change when moving to production from prototype?
Making changes of a magnitude liable to cause such serious accidents renders building prototypes in the first place rather pointless. It was probably a hardware installation error (cable connector not securely fastened, which then dropped loose, chafed wires shorting out...) or incorrect configuration of a fundamentally sound software. I.e. human error during assembly.
There should not be systemic design errors at this point - least of all with the FCS which has consistently been one of the more impressive aspects of the project. Hell, IIRC they even flew it with one of the already tiny tail fins taken off at one point, to test its damage tolerance!