This is not good, because you're modifying the internal self.Cuboid. This causes problems with the selection - the first point and second point of selection get mixed up.

The original code created a copy of the cuboid, then sorted it. It needs to stay that way, the problem is in Cuberite itself, not in WE.

For me, this seem working (see https://api.cuberite.org/cCuboid.html#Assign_1):

function cPlayerSelection:GetSortedCuboid()
        assert(self:IsValid())

        local SCuboid = cCuboid()
        SCuboid:Assign(self.Cuboid)
        SCuboid:Sort()
        return SCuboid;
end

I tested //copy //paste with success

However, I'm trying to repair the issues directly in cuberite