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I remember in previous generations that finding a Master Ball would typically come after a major Boss fight. You could have also gotten through some form of lottery (I think this was in Pearl).
If anything, where and when will I be able to find Master Balls in Pokemon X&Y?
After defeating Valerie in Laverre City, your friends will tell you to meet up near the Poké Ball Factory, at the northern part of the city. After beating Team Flare in the factory, the president of the factory will give you a Master Ball. The Master Ball is obtained in the storyline.
Another way to get a Master Ball is the Lottery Corner found in Lumiose City on Estival Avenue. If you can't find it, just take a cab there. Enter a cab, and pick services, one of the options is the Loto-ID Center, which is the lottery. Matching all five numbers, is a Master Ball, according to Serebii.net.
According to Serebii, there is a lottery corner somewhere in Lumiose City, using the same system as the the ones before Gen 5 (by ID number of any of your Pokémon). I can't seem to find it myself, and I also don't know what the prizes are, but chances are it's still a Master Ball for matching all numbers.
http://serebii.net/xy/dailyevent.shtml
The information is on this page, and it has an image of what the building looks like on the inside.
EDIT: Found it. It's on Estival Avenue.
As others have said the lottery is in Estival Avenue in Lumiose City. It is the city you go to right after the first gym leader, Viola, who is a bug type gym leader, although you can't go there until you save the blackout in the Lumiose power plant at Route 13.
After your friends say meet us at the pokeball factory you must stop team flare inside and then the president of the factory with give you one or you can win the LOT.
The lotto is the easiest way to get master balls with out having to wait to unlock them in Pokemon mart.
