After the USSR dissolved, there was a lot of conflict that had happened due to the messy ways that the Soviet Union destroyed its borders to the point where conflict has gone everywhere from Transnistria wanting to have its own republic to the Nagorno Karabakh region which has had its fair share of wars and conflicts. In 1990, there was even a conflict between Kyrgyzstan and Uzbekistan over two cities.
Of course I don't want to touch around political events today. I wanted to learn more about the historical reasons why this is the case. What was the Soviet Union thinking when it was drawing its borders and did they consider the possibility of ethnic conflict between republics during its lifetime?
I am not an expert, but I can answer re Transnistria. Most of nowadays Transnistria was part of Ukraine until WW2 (and before that, part or the Russian empire). The USSR made Transnistria an autonomous republic of Ukraine as a first step to create a Soviet Moldova. At this point, it was called the MaSSR and included a bigger share of modern Ukraine. After WW2, the Soviet Union took the little part of what is nowadays Transnistria and added it to the rest of Moldova to form the MSSR (a republic of the Soviet Union, independent of the Ukrainian SSR).
Transnistria has never really been part of Moldova, and it’s people feel more Russian and Ukrainian than Moldovans. On a georgraphic point of view, you can see that the border between Transnistria and Ukraine is totally artificial (who cared when both countries were part of the same USSR) while the border between Moldova and Transnistria is mostly natural (the river) as in the old time.
The Soviet leaders used many tricks like that to prevent nationalism. It included moving borders, creating artificial ones, merging peoples, and mixing people from different places of the USSR.
When the Union broke, well... the mess was a natural result of such a strategy.