How can I prevent this script from choosing the same floor twice?

Try this:

local Floors = game.ReplicatedStorage.Floors:GetChildren()

function ChooseFloor()
    local PickFloor = math.random(1, #Floors)
    local SelectedFloor = Floors[PickFloor]:Clone()
    SelectedFloor.Name = "Floor"
    SelectedFloor.Parent = game.Workspace

    table.remove(Floors, PickFloor)
end

Keep in mind you will run out of floors eventually, so make sure #Floors > 0 evaluates to true before calling the function.