Caulk

Did the factory put some kind of caulk in between the lower quarter and the trunk extension? Car started bubbling on the lower quarter area a short while after it was painted. Ordered lower patch panels and trunk extensions and had my friend cut into it and he found some sort of caulk that had trapped the moisture from the car being washed out numerous times causing the rust.....Friend said it was probably done in an attempt to eliminate some of the rattles, also said he had never seen it before.....