I have a lot of little details like this in my main homebrew. Some are immediately obvious, with actual mechanical consequences; others less so.
Halflings don't exist in the setting. Way back in the prehistory of the world, they used to, but they emigrated to found their own world long ago and nobody today knows where they went (very few are even aware that a race of small people called 'Halflings' ever existed in fact).
Fey don't exist at all on the Material Plane of this setting, though they do exist in other planes and even on alternate Material Planes. Sages have theorized that the catastrophe (the setting is best described as post-post-apocalyptic) called the Annihilation so traumatized the world and its natural balance that all the Fey that used to live there died, and with none left to repopulate afterward when the world began to heal- there aren't any today.
Elves have pregnancies lasting two years.
One elf subrace, known for their extremely high power and also for their extreme tempers and arrogance as a result, secretly has human "blood" far back in its prehistoric ancestry- the only signs of which today are the facts that (A) males can grow facial hair, and (B) the race "breeds true" with both humans and other elves- that is, a child of a super-elf with either a regular elf or a human always results in a super-elf. Due to the racial arrogance though, it's not generally a good idea to speculate about those signs in front of a super-elf...
Minotaurs don't have body fat. A well-fed minotaur just looks more muscular and strong than one who hasn't eaten as well. This is because the race was originally bred as weapons of war deep in the Abyss, and are descendents of soldiers left behind by a demonic invasion many tens of thousands of years ago, though no minotaur alive today knows this.
The clergy of the god (sometimes goddess) of Change not only have a custom of electing the head priest of the entire religion every year (in Catholic terms, this would be like electing a new pope every single year with every single priest from the greenest acolyte to the oldest teacher casting a vote), but that priest's first duty upon being elected is to select the religion's official color scheme for the year. Thus, one year the priests and temples are all decorated in red and silver, while the next it's yellow, blue, and orange. This has led to actual mechanical consequences in the form of the "Change Color" spells, which are on the Cleric list. The 1st level version can change inanimate objects only, while the 2nd-level version can change creatures too.
Roadkill reminded me of another one that's so ingrained I never even think about it anymore. The calendar of the world has 16 months of 24 days each, for a total of 384 days- each season containing exactly 4 months and 96 days. The suspicious regularity of this was not a result of divine creation (though some on the modern world think it is), but rather that the Ancient mortals of the Golden Age before the Annihilation were so powerful that they actually altered the world's orbit, as well as the sun's output, to make the standard year agree better with their (hexidecimal) number system.
And regarding that number system, the digits past nine go (in order): dec, mon, dux, trek, quat, fin. (Because the system is hexidecimal, their "ten" is our "sixteen" and their "sixteen" is our "twenty-two.") I drop these extra digits into game conversation now and again when something using the Ancient number system is conversing with modern PCs, and it's always worth some amusement. Particular favorites of mine are when the something in question talks percentages- for example, "75%" in hexidecimal is actually less than half.