He hit the tranny and it made a rattling noise? That can't be good. Or he hit the exhaust and it rattled? The tranny is pretty solid...can't imagine something woudl rattle ont he inside by hitting the outside....maybe a mount bolt is loose or something on the tranny.
So before you got the exhaust tick fixed, was it ticking and rattling, or just ticking. If it went from a ticking to a rattling, I'd guess the "fix" wasn't really a fix. Maybe he didn't tighten the bolt that he added enough....so instead of having a tick (exhaust leak), you not have a rattle, bolt or nut or washer rattling.
Not sure about your exhaust guy, but a lot of mechanics working at the exhaust shops know little more than the oil change techs.