These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Covert Affairs
Anti-Climax Boss: The final faceoff between Annie and Lena. Especially after having a whole episode building up to that one moment.
Foreshadowing: Probably unintentional, but amusing in light of Season 4. In "Walter's Walk", Auggie and Annie have a discussion about what Annie should do in the event she becomes guardian of her nieces:
Annie: My sister wants to make me her kids' guardian. What's the CIA policy on that?
Auggie: Don't tell your family you're on a mission in Colombia.
Hollywood Homely: The embassy representative that Annie must get to turn her remarks that no one pays her any attention because she isn't good looking. Considering a few scenes prior she's wearing (quite well) a cocktail dress that shows off quite a bit, it's... not a convincing complaint.
Vivian of the first season episode "I Can't Quit You, Baby."
Mary Sue: Annie, especially in Season 3. Breaks rules, goes completely rogue on multiple occasions, and never receives any moderately long-term consequences. Not to mention that she manages to outthink the collective intelligence apparatuses of Israel and the United States on multiple occasions. You'd wonder how the CIA or Mossad ever managed to get anything done before Annie came around.
Subverted, however, in the mid-season finale-she more or less completely fucks up, and ends up being transferred back to the DPD, only continuing the story arc because her target is attracted to her and she doesn't know when to quit. Possibly Double Subverted, in that she manages to salvage it more or less completely.
That possible double subversion is given credence as even though the target gets away and the agency gets literally nothing, Joan suggests Annie might get a medal for simply 'getting closer than anyone else'. A fangirl in the CIA even tells Annie she admires her. Though to be fair Lena was also setting Annie up, so some of the good attention might have been played up intentionally and even elaborated.
Some episodes shortly there after suggest that some sort of Myth Arc is forming/has formed around Annie being that multiple agencies are interested in getting close to her (including her own). So where we're at on subverting the subversion for Mary Sue-ism keeps getting spun around as, on some level, the show acknowledges that she's getting special treatment from at least some of her colleagues.
Season 4 seems to be subverting this for Annie. Many of her gambits against Henry Wilcox only partially succeed at best, and at worst blow up in her face, sometimes literally.
Growing the Beard: Around the second episode of season 2, the series takes a sharp nosedive on predictability and safety, starting to feel more like a proper spy show.
Ho Yay: A handful of people are already shipping Auggie/Jai. Well, they are pretty snarky...
Jai/Ben is also being considered. One can certainly interpret things into that look that passed between them at the shipyard...
In London, Annie sits in a park during "I Can't Quit You, Baby" and it's painfully obvious that the park is a green screen.
To a lesser extent, the backgrounds during any driving scene where the actors are in the car talking. This may be a deliberate reference to old Chroma Key spy dramas.
Tastes Like Diabetes: At the end of the first season's second episode, when Annie and her sister resolve their difficulties in an agonizingly predictable and trite way, complete with tearful hugs and comfort food. Thankfully, it's brief.
Most Annie's interactions with her sister qualify: they often quarrel in the beginning of an episode, and their reconciliation near the finish is too far on the sweet side.
This aspect has been toned down significantly in the second season; now her sister and civilian life only pop up when important to the spy aspect rather than being shoehorned into every episode.
Subverted in "World Leader Pretend.'' Annie's sister kicks her out after finding out she's in the CIA.
Thus far into the third season, thanks to Danielle now knowing that Annie's a spy, this dynamic has changed to one of tension where Annie has to balance out telling Danielle how things actually went and telling her the official story. It is suggested that Danielle for her part has often figured out various cover stories but realizes she can't exactly ask what the truth is nor could Annie tell her.