Edit: I misread the first post. No, I've never received a non-legendary in a Master Ball before. But if that were to happen it was probably because the person did what Nexle did and hax'd for them so they have them to waste at their leisure.
And if you don't care about my Master Ball mishaps, feel free to skip the rest of this post. ^^;
I agree that hacking Master Balls is no fun, besides legendaries aren't always that difficult to catch. I think Heatran and Regigigas only took like ten Dusk Balls (maybe less) between them. Those Dusk Balls are my best friend when capturing legendaries. All of mine save for Mesprit and Cresselia are in one.
Back on the subject, I've never put anything besides a legendary in a Master Ball, but I've definitely used them on the wrong legendary before. In Silver I put one of the legendary beasts in a Master Ball instead the much, much higher leveled Ho-oH. In Sapphire I wasted it on a level 40 Kyogre instead of on the Rayquaza I gave up trying to capture because it was tiresome. And even as recently as Diamond, I put Dialga in one, not knowing it's catch rate was higher than other legends. But the only reason I can fathom for the need for a Master Ball in D/P would be if I were catching Arceus, which isn't happening.
Come to think of it, the only time I've used a Master Ball correctly was in FireRed when I used it on Mewtwo.