Aldro on 21 June 2013
Joel lies because it's a test in some ways.
Ellie knows he's not being honest. Why else would she even say "Swear to me that everything you said about the fireflies is true!".
"I swear".
She's afraid of being alone and having Joel swear to her is his way of saying that he isn't going anywhere. She knows it deep down inside and that is why she at the end is okay with it. "Okay".
Also regarding Sales saying Joel was stupid for not figuring it out => During gameplay Joel says they're probably just gonna take a blood test or something. The guy isn't exactly a scientist or a brainiac for that matter. One truly misses a lot by just watching the cutscenes.
