By far the most common “Peter Scar” theory showing up in my inbox is that the Haitian’s power blocking abilities are somehow involved. Which could account for Peter taking damage and not being able to heal.
However I wanted to point out that, assuming Peter survived whatever trauma caused such a nasty scar without his healing powers, a wound like that will take weeks to heal. So unless the Haitian hung around with Peter 24/7 for weeks until it was scarred over, Peter’s regeneration would probably kick in as soon as the Haitian was far enough away.
But again, at some point it will be explained to us, so we’ll see.