Just kidding all better
IGN: "Update: Sony released the following comment to IGN. In short, the problem was actually on Naughty Dog's servers, and it should now be fixed."
"Some players may have been encountering an issue with The Last of Us which affected the autosave feature, which can result in a loss of progress in the single-player campaign. The team at Naughty Dog has been diligently investigating as soon as we heard from our community, and we have determined the cause to be on servers for The Last of Us which were capturing player statistics. We have made a change to ours to address this issue. All players should quit any game in progress out to the XMB and restart The Last of Us. All players can now enjoy single-player and online multiplayer matches as normal."