All current FADEC engine control systems are dual channel, fault tolerant systems (the exception being they all use a single fuel metering valve, so if it seizes it's game over). Single faults are typically no more than an annoyance - on Boeing airplanes the flight crew is not even notified of FADEC faults in flight (significant or serious faults set Status messages, but there are no procedures that tell the pilots to check Status - it's intended for maintenance use). Seeing a minor EPR oscillation and ECAM fault on one engine wouldn't be expected to be a significant concern. The worsening of the EPR oscillation and the problems with the second engine didn't occur until late in the flight - at which point a diversion was probably pointless since the destination was nearby.
Fuel contamination is typically indicated by fuel filter bypass - procedures for gross fuel contamination are based on getting fuel filter bypass on multiple engines. To the best of my knowledge, this is the first time there has been a significant event due to gross fuel contamination that didn't have an associated fuel filter bypass indication.