The thing that jumps to mind for me (the only thing I can really remember) is some really strange "good" luck I had when trying IV breeding in X&Y for the my first little while.
I had this happen to me THREE different times btw. It's just weird.
Ok, so I'll be trying to breed a "perfect" 5 IV Pokemon and I'll be at the last step, but I just won't be having any luck getting exactly what I need. Whenever I do get 5 IVs one of them will be in the wrong stat or I'll have the wrong ability or gender or whatever. This continues on for something like 30 eggs, even though the probability is like 1/12 of me getting what I want. Then finally I get what I need... TWO OR THREE TIMES OVER. You see, when IV breeding I hatch 5 eggs at a time, and what'll happen is after going forever not getting what I need, I'll finally get what I need... twice. In the same batch. Or in the case of my Gengar I was breeding, THREE times in the same batch.
So I end up with duplicate perfect Pokemon. The thing that really kills me though, is when I do the ratio of perfect eggs to eggs hatched after I get those batches with the multiple results, the ratios even out exactly to what they should be. So the odds are lined up right... technically. But it does so in such a way that it screws me over since I only want one perfect Pokemon of that type, not 2 or 3!
Now the good news is that I was able to trade my extras for good stuff. So really, despite it being frustrating in it's way it was still "good" luck. Just trollish good luck. if that makes any sense at all.