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.
Arc Fatigue: The aftermath of the Luther Mahoney shooting in Season 6 started with a newcomer (Falsone) having a burning interest in a police shooting of a drug dealer from the year prior, morphed into laughable dramatics from Mahoney's "long lost sister," and basically destroyed Lewis, Kellerman, and Stiver, three regular characters well liked by the fanbase. Made worse by the fact that the shooting wasn't a black and white issue.
Sheppard's gun-taking fiasco from season seven, which made her look weak, incompetent and untrustworthy. Lewis, regardless if he were justified in doing so or not, looked like an even bigger Jerk Ass who alienated the others against her and even the "good" female detectives turned on her for making them look bad. Even worse, this ended up being one of the seasons' main storylines.
Creator's Pet — Falsone, who solved all of his cases (including one cold case), made up with his wife, and simultaneously successfully investigated every single aspect of Kellerman's Mahoney shooting without attracting any criticism outside of Kellerman. He was brought closer to Earth in Season 7.
Arguably Ballard was a far worse offender, at least initially. The episode in which she first appeared had Giardello and all the members of the unit who didn't get transferred talking about how great a detective she was. The same three-parter had her moaning about how Pembleton doesn't seem to respect her and has Pembleton refuse to follow a completely obvious lead (instead following one that was completely out there) just so that she could look good. Fortunately she became increasingly side-lined (unfortunately in favour of Falsone). Unfortunately she never went away.
Most of Season 6's additions probably also count, with fan-favourites Pembleton, Kellerman and Lewis getting sidelined in favour of storylines involving the newer characters. The TV-movie saw some of these characters get relegated for old favourites.
Pembleton was, and continues to be, Homicide's most popular character. To the point that the only season without him is what killed the series.
Gary Stu — Falsone, especially in the sixth season.
Harsher in Hindsight — In "A Many Splendored Thing" Adrienne Shelly plays the friend of a murder victim who thanks Bayliss and says she is happy to know that if she is murdered, Bayliss will avenge her. In 2006, she was murdered in a robbery of her NYC office.
To further complicate matters, in the series finale Bayliss admits that he 'loved' Frank but it's unclear in what sense i.e. romantically or like a brother.
Let us not forget Munch and his whole obsession with Stan "The Big Man" coming back for an entire season.
Jerkass Woobie: Munch. An insufferable, sarcastic jerk he may be at times but so many bad things have happened to the guy (Being dumped by various women, being bullied in school, being clearly traumatized after seeing his friends shot, and feeling guilty over his abusive father's suicide) that You can't help but feel bad for him.
Pembleton could be a complete jerk but only a person with heart of stone couldn't feel sorry for him after his stroke. Pembleton's best resource was his mind, so his loss of cognitive function is tragic, added to which his wife just had a baby, making his inability to go and work as well as his need to be cared for by her even more tragic.
Felton, again a complete prick but given the way his crazy wife treated him you couldn't help feel sorry for him when he started drinking, turning up to work late (or not at all) and losing key pieces of evidence. And while you kind of agreed (Felton was nowhere near the best detective), Gee telling him that he wasn't good enough for the unit after he'd been shot must've hurt.
Bolander could be a cantankerous old man, especially in the way that he treated Munch. But you felt sorry for the way his wife left him, especially since they obviously still loved each and especially since Bolander finds it so difficult to try and rebuild his life outside of work after losing her.
Kellerman. His wife cheated on him. His partner (and supposed friend) won't open up to him. He's accused of taking bribes even though he didn't. He has a somewhat abortive relationship with Julianna Cox which basically ends because he's such a mess he can't explicate his feelings for her. He kills a bastard drug dealer pretty much in defence of his supposed partner/friend (how was it going to look if Mahoney revealed Lewis beat him up? Plus, he lowered his gun but he didn't drop it) and what does Lewis do in response? Turn his back on him. He eventually gets kicked off of the Police force for killing a total bastard, and everyone he worked with thinks he's trash.
Moral Event Horizon — An interesting example of this trope involves Kellerman. His point of no return does not seem to be the execution of Luther Mahoney, but rather a smaller, quieter scene in which he laughs at a young dead drug dealer on a crime scene, arriving as far as posing for a mock picture next to his corpse. From that point on, the writers portrayed him as increasingly bitter and unlikable - no longer an Anti-Hero, but simply a Jerk Ass.
Det Ballard: We speak for the dead, remember? Det Kellerman: Screw the dead. What have their moldering asses ever done for me?
The latter scene was facilitated by the former, which was such a moral event horizon that Kellerman, who previously quit, started smoking again and descended into bitterness. He somewhat redeemed himself during his guest appearance in season 7, however.
Nightmare Fuel — The episode "Subway." A man (Vincent D'Onofrio) is shoved on a subway platform and is pinched at the waist between the platform and a subway train. We spend the rest of the episode with him as he's waiting around to die. He is lucid the entire time.
Pembleton in the season four finale "Work Related". Aside from showcasing how excellent an actor Andre Braugher is, it is just so damn haunting, from the very realistic moment of his stroke happening to at the end of the episode, where we see the poor guy desperately screaming and pleading for help...while trapped inside of a coffin. This is made even scarier over the fact that, at the time, fans didn't know if he survived his ordeal.
Poor Man's Substitute: The writers seemingly wanted to set-up Gharty as Bolander's poor man's substitute. This is lampshaded by Munch, who claims that a certain trait of Gharty's reminds him of Bolander. However, this analogy falls down in a number of places. For example, while broadly they might be similar (Both are older, in less than perfect shape and fairly conservative Gharty has a number of negative personality traits not shared by Bolander that ultimately make him less likeable (Gharty is a bigot, a coward and usually flirts with Munch's bartender/girlfriend/fiancée/wife). In addition Gharty lets himself get pushed around in ways that Bolander would never stand for.
Replacement Scrappy — Ballard, Sheppard, the younger Giardello, Falsone. Any character introduced after S5.
Season 7's line-up is this particularly because of Pembleton's departure. While Giardello Jr is a decent character (albeit underdeveloped), he is no replacement for Frank Pembleton.
Kellerman at least partially qualifies, being a younger, more attractive replacement for three older, fatter detectives. But unlike previously named examples, Kellerman fit perfectly into the cast and rhythm of the series.
Ned Beatty's leaving meant they couldn't do more with his adjusting to being back at work after being shot. The best they could do was imply that it changed him, as Bolander would never have previously done what he did to get himself suspended.