There are 5000 potential leaks wherever panels join in unibody cars and very common up around the cowl area that takes large amounts of drainage off windshield. The welds are not intended to seal, they use a caulk of varying types depending on location, some is put on melted hot and dries hard. Any cracks later can cause a leak.
After siliconing in a known error place or two and not being happy with the result, I went to using roofing cement like in gallon can from Home Depot. Basically thin cut tar that requires no heat and can be applied with a brush. It dries half resilient yet very firm and will cover dirty surfaces to not leak so much better than silicon it's not even funny. Work the dirt into it and dirt then becomes part of it, silicon requires a really clean smooth surface, you have much trouble getting that in and around cowl panels. Have even used the tar on windshields and no leak ever at any one done like that. Work the area with a small paintbrush to get all contaminants mixed in good and you're done. Messy though. But brother does it work.