While Yamato gets roughed up pretty heavily in canon, including one particularly onesided fistfight with Taichi, and the absolute wringer that Alphamon puts him through that ends with him struggling to stand, he probably doesn't have any scars -- Digimon just isn't that kind of canon. As for Gabumon, while Digimon can't get permanently injured, one of his forms, WereGarurumon, has a whole bunch of scars -- except they're not really scars, just aesthetic markings on his texture.

Eden also doesn't have any scars: He hasn't had time to get any, and while Kingdom Hearts has shown characters acquiring scars before (soz, Braig), it too veers towards the lighter, fluffier, less likely to result in permanent scars side of things 80% of the time too.