My experience has been that this issue is a alignment issue more than likely compounded as you get closer to the end of completion. You do not see the slight miss alignment in the beginning because it is so slight, but as you reach that final meet point all those slight variations have added up.
Yes transfer can cause this problem but normally you can adjust that with the cheater at the very beginning of establishing the girdle on the first few crown cuts. It is really hard to identify an exact issue that you have or had on this stone as your machine itself my be the problem. If you have not encountered this on prior stones you can eliminate likelihood of the machine and more likely transfer or cheater alignment. I use an older MDR facet machine although it has all the bells and whistles except digital it has its manufacturing variances. The quill is slightly off center and I always get some run out as I go around the stone, but knowing your machine you can eliminate that final ugly meet point by adjusting as you go. I would check this on your machine, first make sure the cheater is at top dead center or exactly 0, place a round dop in the quill and check the distance with a feeler gauge at the 4 points on your index. (i.e; 96,48 and 24,72) if they all measure the same distance the quill is centered as it spins around. You do this at 90 degrees with a good master or your polish lap. Hope this helps and what I have learned is getting to know your machine and paying very close attention to length to width ratios on your cutting makes for better and better faceted gems.