The YouTube transcription earlier indicates in passing that the S31 movie was for people who want to learn about Star Trek — which is unfortunate, since it didn’t bother showing much of either the Star-Trek-in-particular universe (other than “We’re in space! There are secret agents!”) or what Trek is about (What, secret agents of different cultures and species can all work together, especially if they all talk like Earth people? Yay).
But never mind even Trek — the surface faults have all been gone over in detail, but I think the deeper problem is that it’s called Section 31, and features people working for Section 31, but there’s next to no consideration of what Section 31 is. In this movie, Section 31 doesn’t do anything morally ambiguous. It fights bad guys. There’s no reason for it to even BE Section 31, as opposed to just Starfleet agents, or even hired freelancers.