A story just like this comes up in Bury My Heart at Wounded Knee. As it happens, tribal rivalries generally weren't considered when reservations were made. While in some cases, a reservation's boundaries were drawn around existing native territory and left alone (or shrunk, depending how things went), the policy of Native Resettlement and Indian Removal rarely took into account the safety of the actual people being relocated.

It really goes back to the Spanish Missions, in a way. The missions in Texas often forced groups to migrate a fair distance to meet them, such being the case for the Karankawa who were largely settled in what would then be Apache land by missionary efforts. This put them under constant threat of raid by the local Apache, but more often than not, the security of these missions (though they did have defensive walls and guards) were ignored for the purpose of, instead, 'civilizing' or otherwise removing the problem that the relocated natives posed in the first place.

So, back to Bury My Heart. In this wonderful book is the story of a man named Kintpuash, a leader of the Modoc people. As it happened, the Modoc lived on a particularly valuable plot of land in the Pacific region. The Modoc, when it was their time for removal, were pushed onto the Klamath reservation. This nation, the Klamath, was their traditional rival - and on the reservation the Klamath were said to have persecuted the Modoc with all sorts of abuses. The government, however, did not care - the Modoc were out of the way...until they weren't. The Modoc returned to their traditional lands and aired their grievances, and the same thing happened again. This ultimately led to the Modoc War. Kintpuash, as mentioned earlier, is something of a martyr in this - having ended up the only indigenous American executed for war crimes, in a war that was never supposed to happen.

While there was a tendency in the larger scheme to put each nation on its own little plot, these plots were often not enough, and whether two plots were next to one another and were likely to lead to conflict wasn't really considered. One famous example of this would be the Hopi-Navajo land dispute, where the Hopi are essentially right in the middle of the Navajo reservation. Attempts to get them to 'share' were miserable failures, and this dispute is in fairly recent memory for these nations. We're talking there were articles written about this in the 1990s, that sort of recent.

I'm sorry if this answer doesn't seem as full as it can be, but I was struck by a commitment or two that shortened my time. I still believe it answers the question truthfully, fruitfully, and comprehensively, where the conclusion is that the goal of Indian Removal was to get indigenous peoples out of the way of useful land, and so their betterment and having a healthy territorial relationship in the right ethnic neighborhood was scarce, if ever, actually considered. Some ended up sharing space with rivals, others got too little space and were parked next to others without regard. Not all of these nations were rivals originally, but conflict ensued regardless.