Trudy and Hometree
When the humans attack Hometree, Trudy is the only pilot to refuse to fire on it, but her bald gunner goon saw this refusal and questioned her about it, with Trudy stating "I didn't sign up for this shit".
So surely the RDA would've had their suspicions about Trudy being a treehugger and Na'vi sympathiser like Sully and Augustine, right? So why didn't they throw HER in the brig with them as well, if only for disobeying orders?
Is it possible they allowed some people to run free who objected to their plans? So they were just keeping an eye on them but slipped up with Trudy unexpectedly releasing Sully and the others?