Originally of course there were 18 universes, but 6 are now gone, destroyed by Zeno because they annoyed him in some unspecified way. Zeno has the power to instantly wipe out anything, and is more than willing to use it. He may look cute, but he’s death. #HistoryofEver 
What was the sin of the 6? Who knows. Still, at the start of the manga version of the ToP, Zeno is disappointed at the lack of growth in the “Mortal Level” of most universes, saying that without growth there’s no point in having 12, and that keeping track of them all is a chore.
This prompts the Grand Priest to suggest they reduce the number again. Lack of Mortal Level growth might therefore have been the cause of Zeno knocking 18 down to 12. It’s unspecified when this destruction occurred, or if the 6 were destroyed all at once or at different times.
(The Viz translation glosses over the suggestive また/“again” from the Grand Priest)
Obvious fan question no.1: does 17’s wish at the end of the ToP restore these six universes as well? So far nothing’s been confirmed. And probably nothing ever will be (still, you heard it here first folks: Granola is from Universe 18).
Whis explains that universes whose numbers add up to 13 are paired. So U6 and U7 both contain Saiyans, Namekians, etc, while U1+U12 and U5+U8 have the highest Mortal Level and were exempt from the ToP. Obvious question no.2: how’s this fit in with there originally having been 18?
Perhaps the 6 destroyed universes were all pairs and the surviving universes were then correspondingly renumbered. So the current U1+U12 combo might have originally been called U1+U18 (and if 17 hadn’t wished right at the ToP, they might’ve been renumbered again to U1+U4).
But to be honest, the “paired universe” idea seems to have fallen by the wayside a bit. You might at a stretch see a parallel between the U11’s Pride Troopers and U2’s magical girls, but that doesn’t explain why U2 has a Yardratian.
Still, this is the reason why the universes are depicted in pairs of matching colors.
Tomorrow: Zamala files a patent.
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