Having a limited edition of 1500 machine does not mean that their numbers go from 1 to 1500, they don't have to be consecutive and they obviously are not.
That being said, having 2 1939 can sound disturbing. Have you reached out to the seller of the other 1939 and asked him how he got it. It clearly is a special request number, the question is did he do the same as you and asked JJP to get it ? Did he go through a distributor ?
Could it be possible that JJP has nothing to do with this confusion, and that someone made a copy of the sticker or edited the number ?
There is no other "certificate" provided by JJP beside that sticker (or at least I didn't get any with my 75RR), so there is more plausible explanation than simply being JJP mistake.