I'm thinking he was reataining water.. Wet. usually when they retain water like that, it does look like blood clots even though it is not.. When I read he was sitting in some water under the shell, that was the first clue but I couldn't get confirmation of if he was sitting in water because of the bator or if the water came out of the shell.I'm thinking that perhaps what the OP was seeing were areas where the chick had nicked a blood vessel trying to pip/turn around. So they weren't actually "blood clots" in the clinical sense, but coagulated blood trapped under the membrane.