The Power of the Doctor - S13-E9
Stupidity: While on the Cyber planet in 1916, the Doctor receives a call from Kate Stewart telling her to come to Unit HQ in 2022 immediately, prompting her to then reluctantly ditch all her problems she's currently dealing with, to go to Unit. The TARDIS literally has all the time in the universe, so even if she waited a really long time, the problems in 2022 would still be there, so there was no need for her to change plans so abruptly.
The Power of the Doctor - S13-E9
Stupidity: After the crew of the space train have taken out the Cybermen, the Cybermen begin regenerating, which one of the crew points out. This guy seems to be aware of how regeneration works, but doesn't shoot at them again. In the series, it has been shown that shooting someone during a regeneration cycle will kill them instantly, but this idea is never considered.
The Power of the Doctor - S13-E9
Stupidity: When Yaz finds the huge Dalek drill, she starts saying everything she is thinking aloud, commenting "They're already here. Seismology. Volcanoes. Daleks, and the Master. This is not good news." There is absolutely no reason for her to say this out loud, considering that she is completely alone and saying this could've risked her getting caught.
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.