The second-in-command of the Crimson Fleet, Naeva Mora, is an intensely dislikable character. She seems very brash and unsuited to such an important job in a "difficult" group - and she is. Naeva isn't a case of Crouching Moron, Hidden Badass or poor writing, she's just thoroughly incompetent. The potential undercover player isn't the first unvetted recruit she's brought in, she isn't subtle enough for complex operations and doesn't plan them well, and her toxic interactions with her subordinates likely have a lot to do with the multiple defections. If you take everything she says as bad advice, you'll go far and it explains a lot about the woeful state of the Key that this is the "first mate".
The terrormorphs you fight in the ruins of Londinion are all scaled to your level, with one exception: the one whose birth you get to witness, courtesy of the Lazarus plant. It's fixed at level 10 (the lowest a terrormorph can be), most likely far below your level at the point you reach this mission, but it makes perfect sense — it's essentially a newborn and appropriately weak.
While certainly annoying from a gameplay standpoint (especially when The All-Seeing A.I. decides it doesn't like you), Commander Ikande's animosity should you start a mission and choose violence makes sense in-story. He makes it clear that the brass thinks this whole crusade is a waste of time and resources and his request to the Vanguard was intentionally vague. After that, you are basically an off-the-books operative conducting all kinds of illegal activities, sometimes on foreign soil. Now he has to admit to his superiors that he hired someone who just went and killed a bunch of people in service to a cause that they don't believe in. Of course he's pissed. And to add an element of Fridge Horror to the situation, the digging around you do in the questline reveals that, while the Crimson Fleet is certainly a problem, it's in dire straights and doesn't become a serious threat unless you help them find Kryx's Legacy.
One of the Alternate Universe starts in the New Game Plus scenario is one where you walk into the Lodge to a dying Sarah Morgan, who calls you a monster who brutally murdered Barrett. As she expires, an Evil Twin shows up behind you to gloat. If you engage in dialogue with your alter ego, one thing that gets mentioned is that this particular version of you tried being the Nice Guy for a couple of universes, and got sick of it, deciding to brutally murder all of Constellation this time around. Not unlike many bored players of Bethesda titles choosing to quicksave before going on a mass murder spree with zero consequences and using reload (or in this case jumping to another universe) as a Reset Button. That version of the player even sounds bored with everything to a degree, but unlike a player, isn't able to put down a controller, instead being forced to go through the Unity over and over again, possibly forever.
