If it's human error I think it must be on the part of the maintenance staff that were running tests before the crash. Surely the ride operator themselves would not be able to override any automated safety mechanism that was built into the ride? I'd like to think it would be almost impossible for human error to become a factor, otherwise the systems are pretty pointless.
I've seen a forum post from someone that said they had added an extra car onto the track to get ready to make up for the delays from previous faults. I can't help think that perhaps they counted the cars at the station and forgot that one had been added...
I do feel a kind of attachment to Alton Towers, we've had annual passes for a year until this May and I've taken my 2-3 year old daughter on a lot of the rides she's allowed on, including runaway mine train. I am really quite over protective with her, and I wouldn't let her on any rides at the seaside or places like that, but I've always thought that AT kept a higher standard and would be safe...