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.
Broken Base: The inclusion of Chase and Nico in Avengers Arena broke the fandom in two. One side hates the idea their favorite characters were sent to a Battle Royale rip-off and Demoted to Extra for a bunch of new characters. The other side, however, are glad they're in anything at all. Whenever or not they're even written in character in this series had sparked some heated debates as well. Hints one or both of them may appear in the sequel only made things worse.
Family-Unfriendly Aesop: Besides its basic premise that almost all adults are evil, or at least highly corruptible or gullible, the series had the rather unfortunate Aesop that one's sexuality or gender identity are subordinate to the greater good - mere minutes after coming out of the closet (and facing a painful rejection from her longtime crush), Karolina is emotionally blackmailed into accepting a marriage proposal from Xavin, a Skrull prince who believes that their marriage might end a war between the Skrulls and Majesdanians. In order for this to work, Karolina pretends to be straight in public, while Xavin takes a female form in private. During Joss Whedon's run, it was heavily implied that both found this arrangement to be demeaning. It was also somewhat more subtly implied that Karolina was starting to view Xavin as an abusive fiancée.
Fanon Discontinuity: Several. Some like to pretend Runaways ended when Vaughan left, others at the end of Whedon's run, some discontinue everything from start of Vol. 3 and a pretty large part would like to pretend there is no such thing as Avengers Arena.
Fashion-Victim Villain: Pusher Man wears a pimp outfit with cape, pair of huge golden gloves and belt with golden PM initials on it.
Harsher in Hindsight: The last issue written by Vaughan and drawn by Alphona has entire staff working on the book answerring the question where they think the Runaways will be ten years from now. One of the comments was that at this rate they'll be all dead, except for Molly. Cut to and it seems the Runaways are now C-List Fodder considering what book are Chase and Nico in.
Hilarious in Hindsight: On the other hand, everybody's jokes about how in ten years Molly or Victor will assemble a new team and the rest of the Runaways will be on some sort of Avengers team have become pretty funny, when in 2013, Victor actually did joined Avengers A.I. Adrian Alphona even joked that one of the members will be a Security Daemon in search of the meaning of life. Victor's team has Doombot with exactly that motivation.
Also, the jokes about adult Molly leading a superhero team, with Craig Yeung even providing her design for Runaways #150 cover, are pretty funny, since a grown-up Molly seemingly did join the X-Men in Battle Of The Atom. Swerves back into Harsher in Hindsight once it's revealed that she's not on the future X-Men, she's on the future Brotherhood of Mutants instead.
Whedongot itwrong became this after Whedon took over Runaways and Vaughan went on to write Buffy comics.
When the Runaways look up supervillains who could be Victor's father, they consider Galactus. Four years later we meet Galacta.
I Am Not Shazam: "Runaways" is NOT the name of the team. Their book is called Runaways because they are runaways. The kids themselves do not have an official team name, usually being referred to as either "The Pride's kids" or "Those kids in L.A." depending on the character. Even some writers have forgotten that detail.
Nico once refers to the group as the Children of the Damned while escaping the convenience store with Topher, though that name didn't stick either.
A fully Justified Trope in the case of the original series - both the Runaways and the Pride make some very dumb mistakes because they're fighting their family.
The plot of "Homeschooling" could have been averted entirely if Victor hadn't decided to hack some stranger's computer. And most of the subsequent drama could have been avoided if the Runaways had kept Chase and Klara separated until one or the other calmed down. It's even highlighted in the TPB, which has a back-up story where Molly suffers a concussion and the first decision the team makes is to isolate her.
One True Threesome: Nico/Karolina/Xavin brings together Nico and K's on-again, off-again tension and Karolina and Xavin's Official Couple status. The closest the actual series gets to this is Xavin offering to shapeshift into Nico for Karolina.
In the wake of Nico becoming evil in Avengers Undercover, some fans have started to float the idea of Karolina having a three-way relationship with Xavin and Julie Power, her most recent girlfriend.
The Scrappy: Xavin and Klara Prast; the former for being a massive jerkass who's role is loaded with Unfortunate Implications (see Strangled by the Red String below), the latter for having a fairly lame power and being introduced in a Bizarro Episode. Both are also hated for being completely out of place on the team (a shapeshifting alien and a plant-controlling time traveler don't match up well with a team of teens with superpowers).
Seasonal Rot: Pretty much everything after Vaughn left the book.
Ship Tease: Nico and Karolina's on-again off-again Unresolved Sexual Tension. Of course, Karolina is canonically gay and has expressed her feelings for Nico. Toned down when Xavin enters the picture but comes back full force after she's Put on a Bus while disguised as Karolina to answer for the crimes of Karolina's parents.
It is even hinted that Nico might have feelings for Karolina and is jealous of Xavin. She seems slightly disappointed to learn that they are still together upon their return to Earth. Nico later tries to undermine their relationship by asking if Xavin's female form is her True Self. She also confesses in a game of "Truth or Dare" that out of all the people she had kissed, Karolina was the best kisser.
Squick: 12-year-old Klara is married to a middle-aged man when the kids find her.
And he abuses her. And when she says that she does not enjoy her "marital duties".
At one point, Klara comments that a psychotic supervillain holding a radio studio hostage reminds her of her husband. Molly doesn't miss the implications on that one.
Strangled by the Red String: Karolina Dean and Xavin. The entire basis for their relationship was that she was a lonely, depressed teenage lesbian, and he was able to become female, and also, they had an Arranged Marriage that had to be consummated or else three different worlds would be destroyed, the result of Karolina's evil parents' machinations. That Karolina had a history of suicidal tendencies gave their relationship some Unfortunate Implications that Brian K Vaughn apparently had no interest in averting (instead of softening Xavin over time, he made him more boorish, arrogant, and masculine, and even had him point-blank refuse to assume a feminine form unless he and Karolina were alone, which of course meant that we never saw it). Even Joss Whedon seemed to struggle to make their relationship look good before finally just making Xavin female. Later on, Terry Moore put Xavin on a bus.
Much of the third series reeks of this trope. Xavin's gender varies depending on the issue, the villains include a crappy rock band and a magic-wielding shock-jock, and the last arc reads like a mean-spirited fanfic written by a disgruntled fan.