I do not know much about this developer, so let me have an understanding of the story out of their own version. They are complaining that MS charged them for patching a patch of a published game, unfair as MS had charged for certification to publish and the patch that followed. And they dont think the bug involved was something that serious.
Now I have to say that I believe it is completely that developer's fault. I said completely, not something like MS did a bit wrong. You release a faulty IT product, that is a fact. You, not your publishing partner, should be held responsible for the loss over the issue. How minor that error is, it is still an error. If it is so minor, why would you bother to correct it? Let's not kid ourselves, FEZ understands that they should patch out the bug (and out of a patch, that is not cool), but they dont want to pay. MS may be not considerate enough to accomodate an indie developer in such manner, but being not considerate enough is not a guilt at all.
Dont try to claim the moral highground by playing with the holy title "indie developer", if you cannot go with only 2 employees, it's not MS fault, it's yours, FEZ.
Youths these days should learn to bear responsibility. When one makes mistakes, pay up or shut up, embrace the lesson to do it better next time. Stop playing with such politics game, that's not a healthy social phenomenon.
Plus, may I add one essential point: MS is the very first one accomodating patching for console games. If you publish on Gamecube / Playstation 2 and have a major screw-up, you may end up being a defendent in a class action lawsuit (god knows what people would sue you for compensation).