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.
Accidental Innuendo: Pete invites Claudia, Myka, and Leena to watch movies with him in his room and mentions his big flat screen TV. He also happens to be in his pajamas.
Averted in the escape from Warehouse 2 with a handwave. Even though Myka finds the wings of Daedalus and Pete makes a good argument, it's plainly clear that having Pete piggyback ride on Myka's back would look... interesting.
Anticlimax Boss: Due to the final season being cut short, Paracelsus's fate is wrapped up very quickly in the first episode. Makes all the buildup beforehand kind of pointless.
Ass Pull: A number of points in the final season, as well as Season 4's final few episodes leading up to it. Notably, Claudia having a sister who was effected by an artifact that Artie dealt with (which needlessly convolutes her backstory), Myka and Pete being 'in love', Artie's son, Claudia no longer wanting to be Caretaker (which seems to get resolved off-screen).
Complete Monster: Paracelsus is an alchemist born in the 16th Century who desired immortality and tested his experimental Philosopher's Stone on his brother's own family to see the results despite knowing the danger. In an effort to achieve immortality, he was responsible for the destruction of a whole village, claiming "sacrifices must be made." Paracelsus was frozen in bronze for centuries until being awoken in 2013 when his brother's family was tired of their immortality and wanted him to remove it. Paracelsus attempted to kill his brother, killing his wife instead. Escaping, Paracelsus went around to hospitals to cure people, but later drained all of them of life to fuel his immortality.
"Running Up That Hill (Deal With God) by Track and Field, during the scene where we discover that Steve is really working for the Warehouse, and is subsequently killed by Sykes for no good reason at all.
The Firefly Effect: Leena got hit by the character (as opposed to series) subtype of this.
Foe Yay: Artie and MacPherson. It really seems like this in "Mild Mannered" when MacPherson's ghost is haunting Artie and they reconcile with one another.
Fridge Logic: In the finale episode of season 3, why didn't HG just put the force field around the bomb when it was clearly stated it can contain the blast?
One of the producers said on Twitter that H.G. couldn't have known if the force field would hold when it was directly over the bomb. When you think of it that way, a blast that big in that confined of an area probably wouldn't be a good idea.
Indeed, it stands to reason and simple physics that containing the blast would have been more taxing on the shield and rapidly used up the power, whist allowing the blast to dissipate outwards (destroying the Warehouse in the process) would have meant less of the explosion would have been directed towards those within the shield, keeping it running for long enough for them to survive.
Genius Bonus: In "Secret Santa", Claudia offhandedly asks how many piano tuners there could be in the Philadelphia area. This is a reference to the archetypical example of a Fermi problem, a form of estimation based on multiplying estimates to obtain a close approximation of an otherwise incomputible answer. The classic Fermi problem is 'How many piano tuners are there in Chicago?'.
Arguably, the series as a whole; this troper has often figured out what the artifact is before it is revealed in-show from information remembered from history class.
Pete in "The Sky's The Limit". After being whammied by the levitation artifact that has caused several victims to be killed when thrown into the upper atmosphere a short time later, Pete only figures it's a good idea to stay inside or with a roof over his head after Artie suggests it.
The Steinbrucks in "We All Fall Down". They instantly believe Artie despite having absolutely no reason to. They don't even try to verify his story. Keep in mind that this family has been entrusted with guarding this Artifact of Doom since 1517.
Artie in the season five premiere. He discovers that one of the forks that allows a person to exist outside of their "home" timeline is missing, immediately after returning from an alternate timeline where most of the warehouse staff are evil. His reaction? "Huh, that's weird."
Idiot Plot: One wonders how much trouble the gang would have avoided if they didn't have the staggeringly stupid tendency of separating all the time, often in the worst possible moments, and ignoring obvious warnings; and keeping secrets from each other despite repeatedly showing that this leads to the worst possible consequences.. Plus being taken out by civilians in ordinary hand-to-hand when they're supposed to be Secret Service.
Les Yay: Between Myka and HG Wells. Pete even comments that it's like having two Mykas around. Confirmed by the actresses that they were playing it a little bit like they 'were in love'.
Like You Would Really Do It: Myka quitting at the end of season 2. Sorry, Warehouse 13, we've done this dance before with Eureka. You're not going to do it. In the first episode of season 3, she comes back at the end, after helping out with the investigation which just happens to feature a Myka Plot Tailored to the Party. Her apparant replacement, Steve Jinks, gets to stay though.
Ok, Syfy. You killed Artie in the first season finale, but you brought him back to life with the Phoenix. You sent Myka away in the second season finale, but you arranged for her to come back in the next episode. Now you are asking us to believe that you killed an agent, HG Wells, and Mrs. Frederic, and in addition destroyed the very thing that the show is named after? Sorry, but we don't buy it.
Narm Charm: Claudia and Claire bond over..."When I Grow Up" by Garbage. It works, somehow, though.
Nightmare Fuel: Dark Vault artifacts are friggin' messed up. Fun examples include the creepy shifting clown painting, the phone screaming "PICK UP! PICK UP!" and the baby doll that grows fangs when you get too close to it.
Paranoia Fuel: Is that classic book you're reading fiction, or is it inspired by a very real and very evil person that lived at the time?
And this could even lead to possible Fridge Horror and What an Idiot moments when one considers how some of these artifacts were used. Obviously, P.T. Barnum really was a total Jerkass and in it for the money when he used an artifact (that could enlarge body parts and internal organs) to make freaks out of normal people...
Though considering we see how (some) artifacts are created, it may be that in some cases, even the horrific ones, the use of them was unintentional and un (or sub) conscious. So jerkasses they might have been but they might not have been so callous as to mistreat others.
Larry 'Noodle' Newley from the Christmas special is also played by a pre-Arrow Paul Blackthorne (Quinten Lance).
Romantic Plot Tumor: The forced "Pete and Myka are suddenly in love" story in an already brief final season was met quite negatively.
Seasonal Rot: Season 5 isn't held in very high regard with the fandom, thanks to being only six episodes long, not having a very engaging storyline (which had the effect of making Claudia's backstory needlessly convoluted), rendering Myka's cancer storyline from the previous season totally meaningless and forcing Pete and Myka together at the last minute. Even the showrunners weren't happy with how things turned out, as Executive Meddling forced their hand on many of the issues mentioned.
Ship Sinking: Usually about once a season or so the show makes a point to remind us that Pete and Myka have no romantic interest in each other whatsoever.
As of the finale, set sail.
Ship Tease: Pete subconsciously wants Myka to have babies.
Also frequently with Myka and HG, especially in the scene where HG sneaks Myka into a police station by telling one of her coworkers by explaining that she's trying to "impress a lady" (the lady in question being Myka).
Squick: In "Vendetta," a set of chains used in the people-stretching racks employed by the Spanish Inquisition has the power to replicate those effects when stretched taut. The viewer gets treated to a surprisingly graphic scene where Dickinson is killed with it, complete with bone-cracking noises as his fingers and legs contort to unnatural angles.
Also how they wrote H.G. off the show — despite her and Myka being a Fan-Preferred Couple for a large number of fans, she gets shipped off to a marriage in suburbia, hitched to a guy we've never heard of before. They do mention in the finale that her and the boyfriend broke up and that she's now dating an unidentified woman though.
The first two seasons of EUReKA centered around an enigmatic, powerful object known only as "The Artifact" and a Nebulous Evil Organization that wanted to control it. What does the crossover with EUReKA center around? Fargo traveling to South Dakota to upgrade the Warehouse's computers, and afterwards Claudia visiting Eureka to study Global Dynamics' technology. This raises several questions...
At least Fargo's visit to the Warehouse was a thematic crossover, involving a fusion of futuristic technology with artifact magic. Claudia's visit to Eureka was basically pointless. The crisis does not involve an artifact going out of control, she doesn't use any artifacts to save the day, and there's really no point to her being there at all, other than some amusing sexual chemistry between her and Fargo...which is left dangling anyway since she never appears again. They could have replaced her character with some random old girlfriend of Fargo's that we've never seen before and nothing would change.
The finale presents us with several scenarios where each one of the agents proved themselves (Claudia stopping an invasion of tap dancers, Myka going undercover in a Desperate Housewives-like suberbia and fighting ninjas, Steve, HG, and Claudia saving Artie from a tiny clock in his heart, etc)...but we only see flashbacks to their resolutions. While it at least avoided being just a clipshow or anything, it was somewhat grating considering how each one could have made for an interesting episode. In particular, when one realizes that in Steve's case, its the only time him and HG actually come close to interacting.
Steve's reconciliation with his mother, and his breakdown over the fact he still can't come to terms with his sister's death, or get past his anger at her killer. Damn, Aaron Ashmore can make you cry.
What an Idiot: H.G. Wells asks about MacPherson's necklace, and he tells her that it's keeping him alive.
What Do You Mean, It Wasn't Made on Drugs?: Played with using Timothy Leary's reading glasses, which cause vivid, LSD-like hallucinations when worn. They were used to find MacPherson's hidden auction of Warehouse artifacts in the first season finale. In "For the Team", Pete uses them to amuse himself when forced into a temporary desk job at the Warehouse.
The Woobie: Pete in "Trial" after his memory gets erased. When Myka is about to confront Eric's mother, you just want to hug him and make him feel better.
All of the main characters, when you look at the backstories we're given about them. They all have dead lovers/siblings/parents, broken old romances, and a general issue with making friends thanks to all of them having some social issues, and that's without the alcoholism, mental institution, troubled family life, or Blessed with Suck superpowers. It makes them bonding together so tightly all the more heartwarming.
The Untwist: Yeah, Jinks is a traitor. Okay. Sure. We believe you.