when Madoka said tells her wish, QB opened his line with "if your wish came true..."
And when Sayaka confirms her wish with QB he told her that "it's possible to fulfill that kind of wish"
suggesting that there is a limit
The way I see it QB is an soft drink dispenser. Once you paid the appropriate price, it can't refuse your demand, unless you put in insufficient funds.
In this case the limit depends on a magical girl's karma. As he said, Madoka being the focal point of the universe, has so much Karma placed on her that could theoretically wish to be god. He didn't expect her to actually wish for something like that.
And from what he said of Sayaka, her potential is bellow average, while someone like Mami had high potential. This could be referring to their karma