Mine's started doing this since it got cooler out, too. Definitely sounds like something on the outside rattling against it - even though I'm not sure that's what it actually is.
Good suggestions on the trim/molding - I'll check mine later.
2012 Focus Ti Hatch | Ingot Silver | 401A, Nav, Winter Pkg, Moon Roof, Parking Tech. Pkg
Build Date: 12/2/2011 | New APIM: 4/4/2012
MFT: Factory v2.11, 3/14/12 USB/Web > v3.0.2, 9/24/12 USB/Web > v3.2.2, 1/24/13 USB/Web > v3.5.1