Someone commented about what they think happened and it, at least to me, makes the most sense:
"It looks like the brake was engaged but the motor kept trying to run, and the applied force synced up with the natural frequency of the structure, thus causing resonance. That is extremely dangerous."
As for why the operators didn't e-stop the ride, apparently Six Flags doesn't allow their ops to do that unless a member of management is present, which seems like a very problematic choice.