Investigators from SEMI (Semiconductor Equipment and Materials International) discovered that the plants were very ill-equipped to deal with earthquakes due to some serious oversights. Some of the more glaring problems included fab equipment that was not properly (or not at all) bolted down, as well as improperly installed piping and ductwork that could cause equipment-damaging water leaks, or inadequate protection against fires.
An even scarier problem is that the fabrication plant buildings themselves were built using construction techniques that make them susceptible to strong quakes. Add it all up and it seems that the Taiwanese semiconductor industry got lucky-- this time. All indications are that, given Taiwan's geographic location (it straddles two tectonic plates) a quake strong enough to cause all of the narrowly avoided damage is likely in the future. Hopefully the September quake and the SEMI report will ensure that if such a quake comes, the industry will be ready.