A lot of times, what happens is that the original polyurethane bead that adheres the windshield to the body separates and rust gets underneath it. Unfortunately, there's really no good way to fix it, and sometimes not even a good way to find it, unless you take the windshield out, sand and prime the rusty flange, and replace the windshield. If you can find where the leak is, there's a slight hope you can get enough of some kind of sealer in there, but don't use silicone: it doesn't stick well to rusty metal, and may make the rust worse. There are automotive sealers made for the job.
Check also for rust spots growing at the forward edge of the rain gutter, and right above it. It's a common spot. If there is a spot developing, catch it now, or you'll end up with nasty holes that are almost impossible to repair, and your roof will leak forever.
