do toi remember this scene ? Norm Spellman tried to stop a Marine who is trying to bring Jake and Grace out of link after the destruction of the Hometree.so why were they sent to jail after wards ?

I find it strange that he locked them up after they asked Parker to go back to the Na'vi. Its as if he was saying, ''Parker gave u one heure to go back & tell tell the Navi to move, but as soon as u get back I'll lock u up".

I don't think it's that strange. It was like a final chance. Quaritch knew Jake had screwed up his original objective, but gave him one final shot to get the Na'vi to leave Hometree.