Why would the vics' faces look so calm if that torture was pre-mortem? The husband especially.
Antonio looks scared when Miguel and Olivia go to leave. (And why didn't they expect that someone might take out a hit on Antonio when they were taking him to the courthouse?)
Elliot and Olivia love Alex so much. The backgammon scene felt almost 'shippy, and then of course Olivia's "It's hard to be someone you're not" could totally be read queerly.
I am just gonna assume that there's a reasonable explanation as to why Elliot and Olivia knew, but the Captain didn't, and that Hammond didn't know that Cragen didn't know.