The formation of the League of Allied Worlds may have brought an end to the Garden Conflicts, but it certainly didn't wipe away a hundred years of prejudice and suspicion. In spite of it's name, the League was never meant to become a unified government for all of the worlds in the Garden Nebula. At best, it was a way for the various planetary and interstellar governments to come together to resolve disputes without armed conflict.
Those early meetings of the League Council were rough; shouting and posturing was seemingly the preferred method of conversation rather than debate and compromise. There was a lot for the Council to work out; planets that had changed sides during the Conflicts that two or sometimes three governments claimed, a interstellar economy and trade treaties needed to be ratified, and then there was the problem of the Allef Refugees. These were just the tip of the gigantic stack of bills, legislature, and diplomatic treaties the Council faced.
In the case of conquered planets; those had to be resolved on a case by case basis. Forty three worlds fell into this category; worlds that various empires had controlled during the last hundred years. Each government would have to pour resources into those worlds, species migrated to those planets to not only secure and protect the world, but also cultivate it or look for a chance at a new beginning. Over the years, the fact that a world held both humans and Naguli populations meant that no matter which empire the world was turned over to, there was a considerable portion of the population that could be upset with the change. This led to concerns over riots and armed revolt; and that happened.
On the world of Barm, the Granos population (about 38% of those living on Barm) objected to being turned over to the Republic of Kel. They protested and formed resistance cells against the Republic government. The resistance groups tried to get the Granos Territories to send help, but the Territories were bound to non-interference by the League Agreement; aiding the Granos take over the world would likely restart the Garden Conflicts. In the end, most of the Granos were offered a chance to leave Barm, and were given a paltry amount by the Republic as a "reparation award". The money barely covered transit expenses, and left those who returned to the Territories with nothing. Meanwhile, those Granos who elected to stay on Barm reaped the rewards, taking over vast amounts of real estate and holdings.
The interstellar economy was an easier topic to resolve; most empires agreed that they would need a universal currency to foster trade between them. Establishing the currency was easy, implementing it was hard. It took an army of bankers and finance experts from every empire to come up with the exchange rates and treasury indexes that allowed the Garden Credit system to come into being as a legitimate currency, and to avoid the inevitable spiral of inflation. The Garden Credit became the preferred currency across the nebula within 5 years of the inception of the League.
The Allef refugees became a complex problem for the League. The Allef were always an aloof race, usually preferring to stand alone during the Conflicts, and only entering the war when they had something to gain. The Allef Domains incorporated worlds from the Republic and the Naguli Empire, all of which were lost during the Conflict's final years. While the destruction of Allef led to the creation of the League, none of the League members could really decide what to do with those Allef who had either been rescued from the dying world or where off-world when the disaster occurred. All the League members were trying to rebuild their own worlds, help their own people rebuild or else handle the waves of refugees from their own empires; ex-patriots who elected to come home when their worlds were turned over to other governments. None of the League members formally elected to grant the Allef any relief, citing a need to focus on their own worlds for a time. This led the Allef no where to go; most had no money or holdings to utilize; those were all vaporized or left behind on Allef. A few philanthropists and charitable organizations did what they could to help the Allef Refugees, but many more slipped through the cracks and had to strike out on their own to survive.
In recent years, some Allef have managed to form small colonies and communities on worlds throughout the nebula, but these are small and widespread. Its still more common to find Allef alone or in small packs, wandering the space lanes trying to survive in a League that owes them everything, yet gives them nothing.