The Research Cloisters is a players wonder, this mean only one per player. However when you upgrade the Research Cloister to a Quantum Research Foundation the Reseach Cloisters become buildable on another world.
And when you upgrade the Quantum Research Foundation to the Ascension Gate on the first world, then the Research Cloister on the second world can be upgraded to a Quantum Research Foundation, and a third Research Cloister can be build on again another world.
So in the end you can have one of all three (all located on different worlds).
The problem lies in the fact that the <IsPlayerWonder> (and other uniqueness) tag works on that improvement only, and that it does not check for the upgraded versions of said improvement.