It seems like Gold has been in charge of this entire thing so I am leaning toward saying that the DNA test was just bogus all around.
I think it’s interesting though that Gold technically hasn’t done ANYTHING wrong here. Emma told Gold that she wanted to work with him and that she was willing to allow him to use his methods as long as it got the desired outcome – and that she was willing to go farther than Regina would. Regina made a deal which was based entirely around the assumption that Kathryn was dead. So Gold worked with the parameters given to him and somehow managed to get what he needed (whatever that is) while getting Emma what she needed (MM off of the murded charges and Emma is now starting to figure out something is NOT right in SB) plus he managed to show Regina that he is more powerful that she is and she did NOT get what she wanted). As a bonus Emma now believes in August and she has figured out not to trust Sidney, and Kathryn isn’t dead!