I need to talk about the parallels between Haibara and Amuro. Specifically in regards to their relationship with Akai.
Both are survivors of the Black Organization who lost someone important to them, and Akai feels responsible for it. The only two times we see Akai, trained sniper for both the FBI and the literal mafia, feel guilt over someone's death. How he has devoted a significant portion of himself to keeping an eye on the person they cared about most in life. And Haibara and Amuro don't care for it one jot because they're missing massive chunks of information that Akai has simply not bothered to fill them in on. Haibara and Amuro who hate Akai and are survivors of his Collateral Damage AOE and it's made even worse by the fact that Akai isn't at all bothered by their vitriol. The two of them slowly learning to trust him and it feels like a betrayal; Haibara to her survival instincts and Amuro to Scotch's memory. Haibara's mistrust of Okiya clashing with her fuzzy memories of Moroboshi Dai, versus Amuro's hatred of Akai clashing with his half remembered partnership in Rye.
Haibara and Amuro wearing matching shirts that say "One of the only people I cared about got killed by the Black Organization and all I got was this asshole stalker, the terrible weight of grief, and this stupid t-shirt."