If you notice on some scenes of the Avengers, whenever Thor tries to take Loki back to Asgard, you can see how his eyes are green as he fights himself. On Stark Tower, while stabbing Thor, look closely and you can also see Loki shedding a small tear.
FACT: This scene was originally done by Tom wearing the Captain America suit. The voice you hear in the scene is Tom Hiddleston's actual impersonation of Captain America. The cameo is Chris Evans impersonating Tom Hiddleston impersonating Captain America.