Yep, sounds like a sloppy windshield install. And to be honest, it's not a fun repair. Your bext bet is to take it to a body shop and let them do their magic. To properly fix it, the windshield needs to be removed and the area affected SHOULD be sandblasted, primed, and painted. If the rust is noticeable, then you can only imagine the damage under the weatherseal.

Trust me, it probably isnt as expensive as you may thinking. It's typically a 1-2 day job. Most of the labor is in the windshield removal and replace.