i haven't had a problem with it. as i do a cutout i have separate containers for the honey comb and the brood/junk comb. if the hive has been in there awhile, the comb is very dark.
when i go to do the crush and strain, i pick through and try to get the dead bees and other bits out before i crush it, but i know i don't get it all.
protein. :-D