Watch the part where Wolverine is fighting the guy throwing the spear-like stakes. When Wolverine charges the guy, the guy stabs him in the stomach. When it goes to Magneto holding him in the air, the holes in his tank top are gone!
that's because it wasn't actually a shirt. It was in fact "Shirtarock the Magnificent" - a mutant from the Wardrobe Klan who very much resembles a shirt and who also has regenerative powers.