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.
Paranoia Fuel: By the tankful; the series might as well be named 101 Ways That Modern Biology Will Kill Us All (When It Is Not Too Busy Saving Our Collective Bacon).
Seasonal Rot: The fourth season is not as well-regarded as the first three, thanks to the far more out-there-speculative main plot (humans have a dormant pheromone-sensing Jacobson's organ, which if activated using a modified Herpes virus can give you what amounts to psychic empathy powers!), the bland and irritating character of Nina, the relative change in character of Bob, and the lack of a proper resolution.
Ship Tease: Caroline is just about the only woman David has interacted with outside of a strict 'let's solve this epidemic now' context but has still never appeared to be attracted to. In a second-season episode, he has a moment of being suddenly sensitive and nice and then kisses her - except that's a Daydream Surprise and when we return to reality David is actually being even more of a dick to her than usual. Sorry, Caroline.
Values Dissonance: For American viewers, the tendency for explicitly religious people on the show to be shown as dangerous radicals or otherwise a little nuts is jarring. That said, Carlos describes himself as a man of faith and he is probably the most normal, nice and well-adjusted member of the cast.
The Woobie: Amazingly, Bob Melnikov verges on this several times but never, ever crosses the line, partly due to good scripts and partly due to great acting.