This article contains spoilers for Doctor Who: Flux.
Timeless Child retcon. But, in the end, the most shocking twist in Doctor Who: Flux was nothing to do with the Timeless Child - it was a single decision reached by the Doctor in episode 6.
The Sontarans had planned to extinguish the final Flux event by tricking the Dalek and Cyberman fleets into being swallowed up by it - committing two acts of genocide. The Doctor chose not only to run with their plan, but rather to go one better - and arrange for the Flux to consume the Sontarans as well, turning a double genocide into a triple one. It was an act worse than any conducted by the War Doctor, not least because she showed absolutely no sign of regret for it. But why would Doctor Who's showrunner make this kind of mistake?
Ironically, a recently-released official breakdown of Doctor Who: Flux has unwittingly explained just how this happened. The breakdown runs for almost 16 minutes, with Chibnall himself and star Jodie Whittaker outlining the main plot, and the most striking thing is what they don't mention. Their focus is on what Chibnall clearly considers the A-plot, the Doctor's attempt to regain her forgotten Timeless Child memories, and her confrontation with the Division. They completely ignore the various sub-plots, including the Sontarans and their master plan. This explains the genocide mistake - because Chibnall's attention wasn't on the Sontaran arc. He took his eye off the ball and messed up badly as a result.
In Chibnall's defense, he was working on Doctor Who: Flux in the middle of a pandemic, which forced Chibnall to change the show's format dramatically. "At the beginning, we weren't even sure we could make a series under COVID restrictions," he itted in an interview with Doctor Who Magazine. "Doctor Who is one of the most difficult shows to produce, and we were aware that [the pandemic] would make it even more difficult. We've tried to keep pushing the show every year, and we didn't want to let the ambition of the show down. But to continue with the previous number of episodes was financially, logistically, and operationally impossible." The episode count was reduced dramatically, and it's notable that - unusually - Chibnall wrote, or co-wrote, all the episodes himself. The pressure will have been massive, and mistakes are understandable.
It may be understandable, but unfortunately in this case it's inexcusable. The Doctor's triple genocide betrays the show's history; although this isn't the first time a script has seen the Doctor do something out-of-character, there's never been such a dramatic example. It doesn't help that Chibnall seems unaware of the magnitude of his mistake, given the fact he's bringing the Daleks back in the Doctor Who Holiday Special - suggesting he didn't even realize he'd committed a triple genocide in the first place. That, more than anything else, demonstrates just how badly Chibnall took his eye off the ball with Doctor Who: Flux's Sontaran plot.