Well, I agree that all of that is annoying, but "Don’t contradict sentences" is not a very good instruction. The construction "A, not B" is not a "contradiction", it's a clarification, a juxtaposition, a contrast. It's self-consistent and non-contradictory.
I have this worded in my CLAUDE.md as "avoid counterfactuals". It still does it anyway, of course, but that language combined with a few rounds of review back-and-forth seems to work for me