Inspired by the comics continuity Nazis thread, I've noticed another problem.
When Brand New Day first happened, there was a two page guide to the changes Mephisto had made. One of these was that while everyone remembers Spider-Man publicly unmasking, nobody remembers who it was under the mask.
However, in the last issue of Thunderbolts where they are fighting the Skrulls a Skrull uses powers similar to Trauma's to make Norman Osborn see visions of being attacked by multiple Spider-Men. These Spider-Men appear in the classic costume, the black costume and the red and gold "Iron Spider" costume Iron Man made for him.
This suggests that Spider-Man still had the same role in the Civil War that he'd had before Brand New Day. Iron Man had still tried to keep him close by giving him a new costume. In fact, if he still received the Iron Spider costume then a lot of the events (including The Other) leading up to that might still have happened as well, even if they were altered.
Isn't this a hole ? Shouldn't Stark be asking why he made a costume for Spider-Man when he doesn't remember who he is under the mask ?
Wasn't there supposed to be an issue of New Avengers explaining how Brand New Day and New Avengers fit together ?