The charge was no small amount as Microsoft charged in the tens of thousands. It all came down to Microsoft's certification policies. Back in February 2012 Tim Schafer said it cost $40k to patch.
The policy had been to charge a studio to initially certify a game and grant one free title update. Every new update would require re-certification and so they'd charge.
In July of last year, Fez developer Polytron apologised to Xbox 360 gamers that had their game saves corrupted by a title update, but seeing as how it affected such an incredibly small number of people it just "Had Fez been released on Steam instead of XBLA, the game would have been fixed two weeks after release, at no cost to us," they said, and any troubles could have been fixed quickly.to spend thousands of dollars to fix it.
Now that Xbox Live isn't quite the bastion for indie development anymore, Microsoft has been made nervous by the vastly more cost effective competitor platforms out there. Many have already criticised the corporate giant for repeating many of the mistakes for Xbox One, but it seems they're coming round.
The certification for Xbox 360 and PS3 updates are notoriously long at times, unlike Steam and other platforms that give greater freedom to the game's creator for being responsible for their products and gamer satisfaction.
Will Microsoft embrace a more open environment with Xbox One when it launches? Indie teams hope so.