The story isn't the reason the Patriots lost the superbowl. It did however cast a negative light on the team. Not that I think the Herald is a stand up organization to begin with, but they had to have known the effect it would have.
Here is a link to the story about the Boston Herald's apologizing for the mistake on MSNBC. ( I am not going to give the Herald any traffic to its website)
However, they have apologized now, and hopefully it will be put to rest so the Patriots can have a great season in the fall.