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>>/8352/
> the latter for being a mistake.
No, there was no mistake. This is the start of the segregation of the tribes; there are no mulattos in Equestria, either you're an earth pony, or a pegasus, or a unicorn.
Imagine that filly growing up, absorbing all the insults hurled at Earth ponies by her parents, and their acquaintances. This generation would grow up firmly believing there was only one way not to put their old foals through that hell -- and that would be to UTTERLY ELIMINATE CROSSBREEDING so there would never be a throwback.
And the only way, really, to prevent mixed genes is to make sure colts and fillies grow up with their own kind. Foals being what they are, they might fall in love with the neighbor.
If this world's magic could support flying earth ponies, or simply had more flightless pegasi like Scootaloo, the foals could direct their parents hate at their own infirmities. But with nothing wrong aside from being born to the wrong parents, they would have to hate their own tribe, or those of their parents' tribe(s).
And by extension, crossbreeds, and the lack of anger and hatred that allowed that brought them into this angry land.