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.
Harsher in Hindsight : In "The Regulator", the villain of the episode faked his own death by suicide to avoid condemnation by his peers. Lucas responds by saying "I can sympathize." Knowing that Lucas's actor, Brandis, would later go on to commit suicide makes for a truly Dude, Not Funny! cringe-moment. It's even worse when you consider the fact that the villain faked his death in 2003, the same year as Brandis' actual suicide.
Arguable, some think the show only found itself during the third season, but too late to save itself. No one, however, thinks season 2 was the best of the lot.
While the plots often left something to be desired, the second season was actually very good with characterization, especially giving A Day in the Limelight to many of the secondary characters. (While the first and third seasons tended to revolve around 2-4 main characters and relegate everyone else to the background.)
Nightmare Fuel: "Knight of Shadows", fitting for the show's Halloween episode. To cap them all, we have a mysterious set of directions, an apparition hurtling Bridger across his room, a man looking straight at the main characters during apaused video, something alternatively setting doorknobs on fire (literally) or freezing them solid for threat of frostbite, and threatening them in general.