I don't have a MT X3, but I had a MT Z3. Same sound. That sound was always there. The pressure plate rattles slightly when not under compression. I personally would not worry about it, but have not heard it on you vehicle. You could always have the dealer do a quick listen, but there is probably no issue.
My garage: 2007 BMW Z4 3.0si Manual, 2007 BMW X3, 2006 BMW 530xi
Retired: 1998 BMW Z3
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