They were using platforms 14 and 15 at Liverpool Street so no obvious issue there, compared to when they used to use the former platform 18.
Do they ever run 12 coach trains at the weekend? They would almost certainly have to run 12-car all day as they wouldn't have the facility to split them down to 8-car at the less busy times. The extra cost of running 12-car trains probably wouldn't generate the additional revenue around the West Ham peak. I note that the 1753 up service from Upminster that I caught was quite busy but it didn't need a 12-car. I appreciate that there will have been services earlier in the day that would have been loaded heavier.
Just as it can be asked why 12-car trains weren't running, is there any reason why passengers don't spread their journeys to avoid crowding? (Obviously there is, but you can see the predicament.)