About the latest episode, I'm kind of rethinking stuff. I don't think it was just Annie who killed Sonny and Bean. I think Reiner and Bertolt were with her when she did them. When I reread that specific chapter in the manga, someone mentioned that it was supposedly be done by two or more people. Annie was just plain unlucky that she was beside Armin during the gear inspection while presenting Marco's gear, making her the primary suspect as the female type titan.
Besides that, I don't think their goal there, in the Survey Corp base, was to kill the two titans, but actually, to kidnap Eren. Eren, after all, is far more important to them that they would stop attacking the wall compared to two random titans being experimented at. If you think about it, why would they risk trying to kidnap Eren during the expedition? They should've at least tried kidnapping him before it.
But as they snuck around the base, they found out that Eren was actually well-guarded(Levi's Squad+Hange), so they couldn't take action. As they left(or doing recon work), they found Sonny and Bean, and decided to kill them because of course, you already know, information should always be kept hidden. Apparently though, RBA are not Armin or Erwin. They didn't think 3 steps ahead of the consequences. The Survey Corp had intensified it's guard around Eren after they killed Sonny and Bean. They just practically lost their chance to get him before the expedition. So they risk it during the expedition.
Just random theories on details though. XDD.
