If i remember correctly, Conan was getting emotional about Andy's last night on the show, and honoring him with some montage or something. Andy was really non-chalant about the whole thing. It wasn't blatant, and maybe i misinterpreted his attitude, but it felt like Andy was holding back a big "fuck you", while Conan was holding back tears.
i remember watching the episode then googling to see if there was any bad blood between the two. i never found anything, but came up with nothing. If someone has their final episode together (torrent or otherwise) i'd greatly appreciate a link.