Heroes spoilers ahead, watch out!
I’m getting a lot of people suggesting that in the future we saw Peter had never saved Claire or absorbed her power, and that Sylar had killed her. So Peter didn’t have the regenerative power, thus the scar.
Sorry, but that’s wrong.
First of all, in the events as they originally ran their course, Future Hiro tried to stab Sylar but it had no effect because Sylar had killed Claire at the homecoming and taken her power. So Future Hiro said fuck that, went back in time and told Peter to save the cheerleader. He went back to his own time expecting things to be right as rain, except now the only thing that’s different is that Claire is alive and in hiding (which is why she’s now alive for Sylar to take her power when we saw it five years in the future), but Sylar is still alive. Fortunately for Future Hiro, Present Hiro shows up on his doorstep. So Future Hiro sends Present Hiro back with the second part of the mission. Now that Claire is saved, Present Hiro needs to kill Sylar. Presumably before he assumes Nathan’s identity and they lose track of who Sylar really is (just a guess on my part there).
So there aren’t “multiple time lines”. There is a single time line, changes in the now cause changes in the future. They changed the future by saving Claire, but not enough to stop the bomb. That’s why Hiro and Ando were confused that New York was still devastated, and went to Isaac to find out what happened in the days leading up to the election that they did wrong. So they could go back and fix it.
As far as Peter’s scar, I have received word that it is not in fact a mistake, and that it’s just something that hasn’t been explained to us yet. Peter does have regeneration, and yet he still gets the scar, and we’ll find out how/why later on in the series. So that takes care of that question.
(I’m not just hypothesizing here. This stuff is paraphrased from a Q&A with some of the show’s writers/producers.)