I have a 2015 Honda Accord. Recently after a rain storm, I opened my trunk to find about an inch of water in the spare tire well. I took the car in to the dealer, and they ran leak tests but they were unable to re-simulate the problem. The car was parked throughout the storm, and I am not sure how the water could have entered the trunk, except maybe through one of the light assemblies, or past the gasket. I know it didn't enter the trunk from underneath (from the roadway). The really puzzling thing is that the carpeting in the car was dry. What could be a fix for this?
If your car is equipped with a sunroof, which I am guessing it is, the drains for the sunroof guides are a common cause of water intrusion into the vehicle. It is expected that water will get into the sunroof area, so sunroof assemblies have channels running front to back that capture the water, and direct to a drain on each of the 4 corners. These drains have long rubber hoses connected to them which direct the water out of the car. The drains at the bottom of these hoses can get plugged, and cause water to back up into the hose and leak from that connection, which would let the water come into the trunk. The dealer may not have performed the most thorough leak test, in which case they could have easily overlooked this. You can have another mechanic check for leaks such as one of the many qualified technicians available through YourMechanic.