Since Emrys has the Sole survivor psych profile, did he ever confront TIM on Akuze and the scientists that tortured Toombs. Did he confront Miranda as well when she told Shepard that Cerberus does,"Good Work." ?
In stark contrast to his general reputation, no. Emrys isn't someone who bites his tongue by nature--he could've been kicked out the Alliance a hundred times over for the way he runs his mouth at his superiors sometimes--but he's cautious with Cerberus because he has no idea what the fuck is actually going on.
When he first wakes up in the lab, and he's trying to piece together scraps of memory through gunfire and blinding white lights, the conclusion that he draws is this is a test. Some sort of training exercise. Induce temporary amnesia, and toss a soldier in a 'captured by the enemy' situation to see how he reacts instinctively. Maybe it's a Spectre thing, maybe it's an Alliance thing, he doesn't remember, but to him, everyone's an actor--or at least, someone who sees behind the curtain he doesn't.
He does think of Toombs, of Kahoku, of the horrors they unveiled, though. In the first proper conversation with Miranda, he has a moment of doubt in his hypothesis, a moment that uncharacteristically suggests suicide as a backup plan--only for him to realise that, if what they're saying is true, and they already brought him back from the dead once, what would be stopping them from doing it again? Over and over, every time he tried to find some escape in death, they'd yank him back up like a puppet on strings. The prospect of that is so overwhelming that he subconsciously doubles down on his initial instinct: this isn't real.
Because of this, a lot of the interactions he has, a lot of the conversations, he approaches as if he were being evaluated, as if he were roleplaying his own life. He does make it very clear at every opportunity that he has no trust or respect for Cerberus, that he doesn't consider himself working 'for' them, and that all of this is done through heavily gritted teeth--but his priority is to do the job and get it over with. So, he isn't going to say something that, in his mind, would be seen as risking escalation in a way that has no strategic value. When Miranda starts spouting her trust for Cerberus, he just opts to end the conversation and stops going to speak with her.
With TIM, he just doesn't see the point. He doesn't doubt that they both know that it happened, and that they both know each other knows. Bringing it up does nothing for the fallen because there is nothing that can be done for them--they're dead. The only thing it would do is alert TIM (and the Alliance, or Council, or whoever is watching) to the fact that Emrys is thinking about it, which would just provide more points of vulnerability to manipulate. He absolutely does snap at TIM for the things that happen there and then--leading them into traps, withholding information, etc.--but Akuze? Akuze is just a wordless 'I know what you did' that underpins the weary bitterness Emrys comes into every briefing with. Also, he isn't going to waste his breath on someone who only smokes half a fag before stumping it out, the hell is wrong with this guy.