Oh, I see what you're saying there, well, I guess you could kind of take what he said a few different ways. Like, maybe he was kind of saying it as a smart a$$ remark as if to say, "If I told you I came from a pirate ship, you wouldn't believe me." OR he was thinking that if he told them he just came from the temple and everyone was dead, they wouldn't believe him. It could be interpreted a few ways, but I think you shouldn't over think it.
The last time we saw him, he was talking to Sawyer and then he took off running through the jungle, presumably towards the temple. Then the next time we see him, he is running through the jungle. I don't think he like time traveled, or went through an alternate reality or anything like that. Just do what I have been doing this season, and accept what they tell you/show you. You will be able to enjoy it so much more.