I think it has something to do with this.

The following bugs have been addressed:

A bug wherein faction leve rewards could be obtained repeatedly without proper expenditure of faction credits
http://forum.square-enix.com/ffxiv/t...ch-1.17a-Notes

From my understanding people were abusing a bug where you could do faction leves over and over without using up faction points. I'm assuming by killing the NM and getting the chest but then "failing" it. I'm not sure of the specifics though.