Sometimes, you'll start out with a good mood for your story-- perhaps it's a post-apocalyptic world with decaying technology everywhere and vampires rule the world.
And then, maybe on a dare or because you wanted a particular plot convenience... you decide that the elevated levels of UV in your world mean the vampires have to wear light colors to prevent themselves from being destroyed.
So now you have your dark, post-apocalyptic, future-tech nightmare world with vampires roaming everywhere.... in pastels.
Yeah. There's a great example of a carefully-planned mood being ruined by an authorial choice that just doesn't fit.
Mood mis-matches happen all the time in fiction, particularly speculative fiction. They happen in movies as well-- how many times have you walked out of a theatre wondering if the director was trying to make a comedy or serious sci fi flick? That's a problem of not fitting into a genre, but it's also a problem of not identifying the mood of the work and sticking to it.
Sometimes, mood mis-fits work really well, and a mood misfit in a secondary storyline can often accentuate the primary storyline (as comedy secondary characters can lighten even a tragic story). And good writing can save anything, even pastel-clad vampires. However, we're focusing on the major elements of your novel, and you want them to mesh as much as possible.
Pull out the list of adjectives you wrote down that set the mood for your novel. You used this list for figuring out your setting climate, and a bit for refining your names.
Read them out loud. Then, take out your notes on your speculative elemetnt. Read your rules out loud. Try describing how your spec element works in your novel. How do you feel when you describe it? Do you want to giggle? Unless you're writing comedy, this is probably a mis-fit. Do you want to brood? If you're aiming for dark and gothic, then good job!
Also look at what you decided to name your speculative element. Whether you call it "the Force," "mana," "warp drive," "lightships," "cybernet," or "lychan," how you name your speculative element has an impact on how your reader will feel about it. Say the name out loud and decide if you feel the way you want to feel when you read your novel.
Some names and speculative concepts will be fairly neutral and may have no impact on your novel's mood. "Magic" is generic enough to require more description if your characters will encounter or use it in your novel. "Magick," on the other hand, leads you to a little sense of mystery, an enigma.
Rename and rework your speculative elements and their rules if you need to.
Here are three examples, one from each broad speculative fiction genre, of the speculative element lending itself to the mood of the piece.
Example One: Science Fiction
I watched Alien: Resurrection this weekend and decided it was a good science fiction movie. Not so much a horror movie, which is what Alien and Aliens were, but a good science fiction movie. There were numerous points where something was explained-- some element of the alien's biology or Ripley's biology were explained scientifically (or pseudo-scientifically if you're unwilling to buy-in to the original premise that Ripley and the alien queen could be cloned). The speculative element was that Ripley and the alien queen could be cloned, but that such cloning would result in their mixed DNA-- a little bit of Ripley would be inside the queen, and vice versa. That element of blending the human and the monster repeated itself over and over, so that this movie's mood was dark and angsty, all about internal conflict, and reconciling the self and the other, and the moments of reconciliation are almost erotic in their presentation. Frequently, scenes highlighted this conflict, especially the most memorable scene, Room 1-7, where Ripley confronts the failed clones, twisted combinations of herself and the queen that are hideous and disturbing, but also worthy of compassion.
Example Two: Fantasy
The Harry Potter books and movies are a great example of a spec element lending itself to the mood. The magic in these books is almost entirely known, out in the open. You learn a spell that other wizards know already. The magical beasts have special powers-- but those powers are known and knowable. There are few real mysteries about how magic works in this world, at least to the experienced practicioners of it. Dumbledore never says "I don't know how to do that, Harry." Similarly, the problems Harry faces are known and knowable-- Voldemort is a known enemy, whom Harry must confront in every book. The bullies at school are known-- Ron never turns out to have betrayed Harry. Navigating the complicated rules of Hogwart's is a secondary conflict in the books, and one which further highlights the main theme of learning how to operate within the rules (and sometimes outside of them) in order to succeed against someone who violates them. Incidentally, Harry Potter is also a good example of a mis-match counterpoint-- many of the magic items and spells have comedic names and functions, and the sub-plots involving them serve to lighten the overall storyline for children.
Example Three: Horror
Good horror movies should scare the audience out of their shoes. One of my favorites is The Blaire Witch Project. Not just because it was groundbreaking filming, but because it set the mood perfectly. At no time does the audience know what is really happening-- and neither do the characters. The force that they are in conflict against is powerful, unknowable, enigmatic-- the mood is one of unknown terrors. You never SEE the witch-- in fact, the most powerful visual impression comes at the very end of the movie, and serves as the only explanation for what is happening. A lot of people leave this movie saying "I don't get it," because the clues and cues are very small, and missing even one means you miss the (entirely non-verbal) explanation. In horror movies where the protagonist wins, the explanation has to come before the climax, but the mood actually shifts at that point and stops being truly horror. A horror story that never completely explains the horror element maintains its mood simply by virtue of never letting the reader know what's going on.