It's really luck.
I mean, assuming the same method of catching was used in Gen V (if it wasn't, something similar at least), and assuming Mewtwo has the same catching rate as most legendaries (3) then the chance of catching would roughly be 7.1% with a bunch of Timer Balls, 3.5% with a bunch of Ultra Balls or 6.2% with a bunch of Dusk Balls.
It's all just considered by luck - you just got really unlucky/lucky in many ways. xD
But you caught it now, so I wouldn't worry. :3
Hope I helped. :)