I don't think they particularly have minute by minute timetables on the MRT, just first and last train times and number of trains operating per line during peak/off-peak periods. On the circle line the trains are driverless and operate with a moving block system (Comms-based Train Control), so the headway between trains is fairly constant, but the absolute timings are dependant on the train ahead travelling at the ideal speed, not stopping for too long etc. (e.g. if someone holds the doors to jump onto the train last minute you'll be delayed as the doors re-open and attempt to close again). So I think you would have to extract logs from the control system or the trains themselves to establish exactly where they were at any particular time. And bear in mind that this information is probably rarely used (at least for this purpose) and may not be in a format suitable for the kind of analysis they needed to do. Funnily enough it was the use (and failure of) of the CBTC system that caused this problem.
Also remember that until they begun the analysis it wasn't clear that a single train was the cause. I imagine they were investigating trackside issues as well as issues with those trains that stopped, rather than an independent train that wasn't experiencing problems.
TLDR; It's not a case of looking at pre-defined timetables.
Sure, but minute-by-minute is not needed.
If you look at the last graph on the page, the one after "The pattern was especially clear on certain days, like September 1. You can easily see that interference incidents happened during or around the time belts when PV46 was in service." it is the most simple data, drawing points (the incidents) over a service timetable.
These data (when the single train was in service or not) must have been available.
I believe that the tricky part was the "delay" between the PV46 passing and (some time later) the "wrong braking" of another train.
Also remember that until they begun the analysis it wasn't clear that a single train was the cause. I imagine they were investigating trackside issues as well as issues with those trains that stopped, rather than an independent train that wasn't experiencing problems.
TLDR; It's not a case of looking at pre-defined timetables.