He was kept separated from the other prisoners, too. During the escape, Zola came out of the same room right before Steve went in and found Bucky who was mumbling something. I did not notice the sniper thing till after the second viewing. Also, I remember reading somewhere about how Stan purposely acted differently. If you notice, Bucky was all smiling and confident at the beginning of the film. Then after the Hydra base, he seems depressed and beaten. Even when they were joking at the bar and the cliff, he seemed sad. Oh, the commentary pretty much gives it away that something was done to Bucky and he would be back. Although, I never thought they would do the Winter Solider story in the first sequel. Better yet, named it as the subtitle of the film.