User blog comment:IamJakuhoRaikoben/Chapter 375: Supernatural, Review./@comment-3424593-20140314111920/@comment-7418318-20140314204500

Maybe he snuck on the airship after Zeref and used his stretching hands to catch Hades' corpse before it went completely overboard.

If Hades had just died less than a minute before he got his hands on him, it'd more sense that he was able to "harvest" the soul from the body.