So whenever I play anything with just a little bass in it on low to medium volume the piece above the rear seats rattles. Upon further investigation, I opened up the trunk and noticed that right above the trunk light bulb and where the sub attached to the metal frame, that whole area just vibrates and rattles uncontrollably (loudly). I stuck my fingers in and held onto the metal frame and it definity dampened the rattle.

Has anyone had this issues? Is there a way to stuff something in around the metal frame that could stop the vibrations? It's gotten progressively worse

There's lot's of ways to dampen sound vibrations. Placing adhesive backed tar products like Dynamat is pretty common. Foam can be put between panels hitting each other. Is this your factory subwoofer or an aftermarket one? I'd ask for help at a dealership if it's factory and I'd check for advice at a Car Stereo shop if it's aftermarket. Checking the bolts/ screws holding things down is a good idea. Body panels get those snap things and those should be snug and are replaceable if loose.

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