Nope, I get Zapdos in my game. I forget what determined your legendary bird in XY, oh, I think it depends on which starter you chose or something like that (I chose Fennekin). That Moltres would have gotten away from you no matter what, so don't worry. You have to encounter her in the wild 7 times (can happen over time and not necessarily all in one play session) before she flies off to wait for the final encounter on a little island in the Northwest called "Sea Spirit's Den"