Spoilers on 34th chapter of manga.
Right after capture of Annie, Erwin came to conclusion, that there may be more shifters in this squad. Therefore, he decided to keep them in some isolated place. Real reason, why they are in isolated place, was hidden from squad, and they were just told that they are patrolling, yet almost all squad was wondering, why they are in civil dress and without any equipment, while other Survey Corps members were in full equipment, and were looking nervous.
Spoilers on 42nd chapter of manga.
It is not exactly clear, when this occured, but on certain moment, Hange and Armin came to conclusion, that Bertolt and Reiner may be titans, as they've came from same "village" with Annie, and possibly were cooperating with her.