Historically, discrimination has been fed by a ruling class looking to divert attention away from any perceived failings. The capital city burned down in a raging fire? I saw a member of group X with a match, it must be them! Widespread famine across the countryside? It's those greedy Y's hoarding all the food! Rampant economic instability? You know it's the Z's with all the money who are behind it! Whether the ruler was actually at fault or not, their legitimacy derives from their ability to keep a stable country functioning. The best way to save that legitimacy is to shift the blame and punish some "other" group. In that way, the non-other subjects can feel a sense of justice or rightness in the world, while the ruler does not have to answer any hard questions about what actually went wrong. The "other" group that is targeted is usually not a coincidence. They might be politically troubling to the current ruling class, or have property that is desired by the non-other subjects.
Without these dynamics in the game, I see little reason for such tensions to exist. The closest thing I can think of would be to tie it in to villainous plots. I imagine it manifesting in historical events like these:
"In the Spring of 149, "Mountainhome: Fact or Fiction?" the leather-bound codex was stolen from Hatedrashes. Despite having no evidence, King Snodub LanguishedBuckets blamed dwarven collaborators for the theft, inflaming tensions between dwarves and goblins".
"In the Winter of 263, Urist McChild was kidnapped from Abbeycrystals. When witnesses reported a coincidental visit by monks of the Lilac Council at the same time, an angry mob razed the temple to Dunem as the militia stood by"
Of course, the events to precipitate such public outrage against the "other" must be sufficiently severe. Maybe when sufficiently valuable artifacts are stolen, a check could be made for groups that the ruler may want to blame. Maybe the same for when important people are kidnapped.
However, until such tensions are modeled in the game, I see no reason for there to be minority groups gathering in an enclave. With nothing to fear from the ruling class, the minority has no reason to separate itself.