You can actually get 2 masterballs.
When you enter misralton city,you will meet professer juniper and after you finish talking to her she will give you a masterball.
After the player enters the Hall of Fame, Colress is still dwelling within the Plasma Frigate; however, he and the other Team Plasma members have decided to put an end to their ambitions. Colress will battle the player once per day. The first time he is battled this way, he will give the player a Master Ball.
The lottery masterballs:(many)
The lottery is one of the shops in join avenue that can be built, but unlike the other shops, you don't make any purchases. Instead, you just get a chance, once a day, to win an item. As you rank up the Lottery stores, your chances of getting the top prize are increased.When you get first place you will get another master ball and so on!!