Yep. She mentions in the manga that having a magical girl's Etheric body means that while she's much stronger and more durable than a regular human, particularly deep wounds don't heal properly and leave scars. They're most visible in her dark form, as seen here.
Indeed, the noticeable ones are on her right arm and her left hip. She usually changes clothes using her wand as if to hide them, and does normally dress to avoid showing them (IE, always wearing long sleeves to hide the ones on her right arm).
Right now, Momo is a half dark-aligned and half light-aligned Momo!!Wha... What the heck, that's so cooool!!Momomo~n...
