Naruto and Iruka had an argument when the latter refused to give recommendation of the former for Jonin title, which goes against the rules of the village that one must go from Genin, Chunin and Jonin in order. This cause Naruto to pull off a tantrum and run away.
Sakura essentially telling Naruto that she wished Sasuke was around instead of him. It hadn't been a good day for Naruto up until then, as he had started to feel the full weight of not having his parents around (again). Then Sakura dragged him away just to complain about hers (which you could tell was starting to actually make him angry) and then she hit him with that. Keep in mind that Naruto has pretty much gone through hell just to get Sasuke back for her and himself so that comment was extremely harsh. Not to mention that Sasuke had deliberately chosen to abandon her and the village. Had Tobi not shown up immediately after to kickstart the actual plot of the movie and take their minds immediately off of that, the two's friendship likely would've been irreparably damaged.
Sakura finally coming to terms and understanding what Naruto had been feeling his entire life. It took a few days but to see how lonely it has been for him to not only grow up and live without parents but to see everyone else be with theirs took a heavy toll. And when she ran to say she was wrong and wanted to go back, she found him with his parents, enjoying life as a family for the first time. Thus, she now had two weights on her back. Either stay and be miserable so Naruto keeps a family for the first time or go back to her own family while Naruto is once again alone.
Even better, Naruto made the choice for her. He really didn't want to leave but knew this world was not his own and he and Sakura still had family back in his main one.
Really, just the concept that AU!Naruto having two living parents with whom he lives a happy, normal life is what makes his life so bizarrely different from the real Naruto's. One scene has Naruto finding himself eagerly running home because he realizes that, for once, someone will be there to welcome him. He returns home to find his parents getting ready for dinner and happily greeting him. What would be a mundane event for most people almost brings Naruto to tears, because this will never happen in his actual life.
