Are you sure the extractor part of it is larger than the bolt that went in?

Also thread that extractor tool into the crankarm as far as it can go before turning the extractor nut. Make sure the extractor nutis not protruding the attatchment nut as well when inserting, so you can ensure full insertion.

Also is the extractor nut going in as far as it can go, or is it just not able to turn at a certain point?