The sort of numbers is defined by your chosen output style. Perhaps they are alphabetical, rather then ordered by appearance?
What publisher are you targeting this for? Perhaps there is already an output style you can switch to that orders them and lists them according to their criteria?
Numbered style should list them in order of appearance (unless they are cited again later, and then it will reuse the earlier number. – Also, make sure none are in text boxes, which will force them to be numbered first.