It's easy to point to the Patriots three big miscues (blocked punt, pick six, punt return for TD) as the reason why the Eagles were able to leave with a victory. When looking through the play-by-play, it turns out that the Eagles defense did better than expected.
There are some negative plays that were self-inflicted, including the big turnovers and special teams play calling and mistakes. There are also the seven 3rd or 4th and long situations that the Patriots were unable to convert. There are tackles for loss, sacks, penalties, and defended passes.