In the process of building a car, you take a whole bunch of stamped sheet metal components, fixture those sheet metal parts into to a precise location then spot weld the components together to form the shape of the car's autobody. The easiest way to fixture parts accurately is to use punched holes and slots as locators for pins in the weld fixtures.
Remember when your car is welded up, those panels must be accurately located to the nearest 0.2mm or better. (My best guess... depending on which part of the car we're talking..) Generally those holes are located in dry zones within the vehicle shell. If the hole happens to be on an outer panel and a water tight seal is required, the automotive manufacturer will use a rubber or plastic grommet (plug) to seal up the hole. Those grommets tend to be hand installed at the vehicle assembly plant after sheet metal is welded.
It looks like somebody missed that plug on your rear trunk inner panel. You can remove the plastic rear cover from the trunk, accurately measure the size of the open hole, then order a replacement grommet / plug (either from your local autoparts store, or directly from the dealer.) As I examine the photo of the hole in your sheet metal, it looks like there was a plug installed at one time... I can see the hint of black line where the edge of a grommet would sit. Could someone have remove it for some reason? Perhaps it was partially installed and fell out later? At the the automotive plants I've worked, they did do a 100% test for issues like this.. we used a water booth system where every car was sprayed as though in a hurricane rainstorm for five minutes, then they'd inspect for leaks inside the car. If totally missing, this would have been caught for sure.
If the car is new, this should definitely be covered under warranty.
Note: sometimes you will see a wire harness pass through these holes, with a molded on grommet already on the wire harness. Note2: They've been using this stamped hole / grommet seal technique for more than 50 years or so.