For you out there. I know how to get more than 1 Master Balls.
#1: Go to the department store and talk to the lady on the left for lottery (I think that you have to defeat elite 4)
#2: Give your only Master Ball to the lead pokemon and go to defect elite 4.
#3: Go to the Team Aqua and the Team Magma base and defeat everyone in there but you have to collect all the things in there include a Master Ball.
Hope this work for you guys/gals out there as for me.