There is a crippling autosave bug in The Last Of Us. Often the game will hang during autosaving and instead just read “Autosaving. Please wait…” in the pause menu. You can still play and make progress, but none of it is saved. If you’re like me and playing on a hard the first time through, not noticing the glitch can be pretty brutal. I lost all of my progress through chapter two as well as half of chapter three. Since then I have been pausing the game every minute or so to check if autosave is still functioning. I have noticed the autosave seems to hang when cut scenes are played. I don’t know if those are the only times it will hang, but those are the most obvious times I have noticed.
I hope Naughty Dog patches this soon but for now keep an eye on the pause menu and good luck.