Malnutrition. (Abyuser) Mister starve her until her paste starts turning black (like dead yukkuri, probably their equivalent of necrosis). Moreover, the skin became translucent so you can see her inside turning black.
and new Chapter you will see why this happen because anon are inexperienced lacking knowledge how raise pet yukkuri plus he bussy he forgot yukkuri some times.
Anon he Dont had patient tell them become good yukkuri or will get punish. will there one good yukkuri that marisa and his two sister reimu are shithead.