As someone who spent years studying the design of roller coasters before choosing an engineering discipline elsewhere I have a lot of interest in this incident as it seems to have been either a computer control malfunction or operator error (or indeed, both concurrently).
To assess incidents like these (and I assume in the rail industry) a fault tree analysis is undertaken to work out firstly the possible permutations of the incidents that could happen to safely design them out or mitigate for them, and secondly after an incident to work out the issues that caused the event, also known as the antecedent.
The thing is these systems have limitations and it takes great engineering expertise to work outside the box. One thing that people are seemingly forgetting it that there are two events here, both of which shouldn't have happened. The initial "stall" of the cart in the batwing element is a big event. It would require the entire section of Alton Towers to close and the ride cart either be dismantled on-site, or to be craned through the ride to the next block section, which on The Smiler, is the second lift hill.
This first incident is worrying and rare enough to warrant an investigation. It had also happened before in the same section, an area of the ride known to have profiling issues.
My point is that there are so many reasons that could have caused the incident that it's hard to speculate outside of a few good guesses, but the fact that there is a single incident (the valleyed cart) that escalated when the passenger cart was released from the top of the lift hill (which, it should be noted, is correct procedure when the following block is uncleared) shows that there has been a catastrophic failure of processes.
There is evidence to support that it might have been an operational (human or technical) error in this instance though; Merlin have suspended operations on three other rides, one of which is built by the same company as The Smiler.