Quote 1
I laugh a little. "Calm down? Calm down? That's my family they're talking about, that's my faction!"
"No, it's not." There are dark circles under his eyes; he looks exhausted. "It's your old faction, and there's nothing you can do about what they say, so you might as well just ignore it." (19.18-9)
Will prevents Tris from fighting with Molly and Peter. Molly's been lying to the Erudite newspaper about how terribly abused Tris was by her family, so naturally Tris wants to attack. But think of it this way: Tris were a good Abnegation member, would she want to attack? Probably not; so, by attacking, Tris shows how far she's traveled from the family that she wants to protect.
Quote 2
"Is he right?" Will asks quietly. "Are you trying to manipulate us?"
"How on earth would I do that?" I scowl at him. "I'm just doing the best I can, like anyone else."
"I don't know." He shrugs a little. "By acting weak so we pity you? And then acting tough to psyche us out?"
"Psych you out?" I repeat. "I'm your friend. I wouldn't do that." (21.45-8)
We know Tris isn't manipulating her friends. But it must be super weird to be friends with people most of the time and then try to beat them into unconsciousness the rest of the time. No wonder Will is unsure if he's being manipulated.