The last scene where Sam says Dean is in trouble, am i the only one who didn't get that line? I mean how did he realise that? Did he overheard what Cain told Dean? Cause Sam have believed in Dean so far, what made him think that Dean is in trouble?

He was trying to say how Dean did well, he is feeling victorious, Dean saved the day and stayed himself, he handed the blade over. 

and he said 

Now look at Dean, and look at his eyes, and look at that from the eyes of the person who knows him better than anyone: 

This smile isn’t genuine. it isn’t a smile of victory or success. this smile is only trying to reassure his little brother. 

But he can’t play this all along: 

and he looks at Sam, and there is pain, and he is worried so much, and he doesn’t believe in it really, even though he try. hetried but then he said ‘maybe’ because Cain’s words are still in his mind. 

And now look at Sam’s body language: 

He is leaning back, absorbing, realizing Dean is not okay. at all. knowing the hope he has isn’t something Dean shares, knowing the victory he feels by defeating Cain, isn’t a victory Dean shares. 

Knowing Dean isn’t alright. 

Next thing Dean is asking for ‘rest for four days’ . 

Sam knows how to read everything about Dean. He can’t be fooled.