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.
Fridge Brilliance: In Diabolical Box, there's a minigame which involves a hamster. The hamster speaks throughout the minigame, and also afterward, when he becomes the coin- and hidden puzzle-finding companion. This is a little jarring...then you remember that Luke is the one who is supposed to be interacting with the hamster, and Luke has the ability to communicate with animals. The hamster "talks" because Luke can understand him!
To put things into perspective, the first game was released in Europe nine months after its American release. Due to its success, subsequent games were always released around one month after the American release, with Miracle Mask taking a two-day lead in Europe and culminating in Azran Legacy coming out in Europe in 2013 and in America in 2014.
Not necessarily... Emmy states that Bronev might as well have been her uncle actually, so odds are they're not actually related.
Ho Yay: Luke and the Professor seem a little too chummy the vast majority of the time, although it can easily just be read as a Bruce Wayne/Dick Grayson arrangement. Then again, that one has similar problems...
Somewhat lampshaded by Chelmey in Diabolical Box, who decides not to probe too deeply into the relationship.
A devianart user (explaining a fan belief to someone unaware about the series): Like... he wasn't a good parent to Flora because he almost always leaves her behind (he's really concern about her well-being and he doesn't want her to get hurt pretty much) and from the spin-off game Layton Brothers, he has a son name Alfendi and they believe he didn't raise his own son right as Alfendi picked up his father's hoarding habit (that and Alfendi's pretty much a psychopathxDD). Of course, there's his self-proclaimed assistant Luke and Layton just lets him waltz in casinos and Layton's just putting his best friend's son in peril pretty much.
Anthony: Oh, and if you get stuck, don't bother asking me for any hints. I'll provide nothing of the sort! I want you to solve this puzzle in its... purest form.
The Chocolate Code in the English version of Curious Village. This one wouldn't be so bad if the translators hadn't changed the hints so that they didn't reference the most significant part of the clue's illustration.
One of the bonus puzzles in Diabolical Box asks you to multiply a three-digit number by a one-digit number to get a four-digit number using the numbers from 1-8 only once.
Ships That Pass In The Night: Flora and Clive. The ship potential is there, but they don't interact much unless you count Clive kidnapping Flora.
Spoiled by the Format: If several mysteries are not yet solved, you likely have a way to go, and you certainly do if not all of the mysteries have been found. Additionally, the number of puzzles for each game gives you some idea of how far you are when the number of a given puzzle appears.
They Changed It, Now It Sucks: Layton 7, which is basically Professor Layton In Name Only. As in... in name only to the largest degree you can possibly get, to the point of being a non traditional puzzle game that doesn't star Layton, has a new art style and is made for both 3DS and smartphones.