As a sound competitor, any time you install aftermarket subwoofers, you will almost always have trunk rattle. That being said there are things you can do. Sound deadening being most of it. You can use dynamat, fatmat, or i suggest audiotechnix just because of the cost. its about 70 dollars shipped for 25 sq feet. That much should be more than enough to get rid of alot of trunk rattle. Also look at using a mild spray foam into small areas of the trunk lid that make an "air pocket". any other questions please feel free to send me a PM
Also seeing as its a sedan try firing the subs into the car. This will help the subs pressure load into the car instead of just the trunk.
As for it being certain notes. The lower the note the more the rattle. Lower note means longer wave length. Making more chance for things to rattle.