Is it the yolk sac? It normally fully absorbs before hatch. Hopefully someone more experienced hatching eggs will chime in. I have only hatched a handful, and only with broodies (but 1 was assisted due to early crack in egg) and never had that problem. I have seen on here where they have put chicks in a cup. I think it was to immobilize them a little while the yolk sac absorbs, but I am definitely not an expert and can't really advise.