i have a bad feeling that this is because your starting square was imperfect.
as proof of principle, try doing the same steps with a regular square of kami. if it comes out alright, it is indeed because your starting square was off. if your square was fine, it is most likely because one of your earlier landmarks was slightly off.
nevertheless, i do think it should be possible to proceed anyway. everything will not necessarily line up correctly, but you will be able to get a gestalt of the folding sequence to try again later.