Honestly, to blame the controller after the automated system has failed is pretty low. The system does not run this way normally for good reasons, and whilst the controller maybe trained to handle the situation they won't be well practised at it.
The primary reason is computer failure followed by the decision to run the system manually.
When computers fail here in the Netherlands, trains are just stopped until they can be fixed.
In some cases, trains can be ordered to drive "at sight" -- slow enough (walking speed, basically) to stop if there's something visible on the tracks that shouldn't be there (train, car, person, cow, whatever)
loading story #50278737
loading story #50276948
Proper training focuses specifically on those exceptional situations (like it does for airplane pilots), with strong emphasis on always falling back on safe procedures. Even so, you can't cover 100% of possibilities.