There are several things that can cause this.
1) Sometimes one of the screws inside the controller will come loose and start rolling around inside.
2) There are some plastic parts of the controller inside that can break off and cause this noise
3) Sometimes something can fall inside the controller near the triggers. While this is not common it can happen.
Ultimately if the controller is still working it's probably nothing to worry about. If, however, it's driving you nuts you can always just take the controller apart enough to dump out whatever is in there making this noise.
Hope this helps.
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