Vibrating Sound in Cabin & Dust issue

I have driven my Prius C around 28K Miles in almost two years. Recently i am facing two issues with it and i have no idea how to deal with them please help me out.

1) There is a constant vibrating noise coming in cabin from doors and glove box. it is very annoying checked for lose material but found nothing, is it possible my doors got loose due driving on bumpy roads ?? how to resolve this issue?

2) Second issue i am facing is related to sealing of car. Outside smell and dust is entering in cabin even AC off and fresh air damper in closed position. what could possibly the point of intrusion.

Both these issues arose after i had to drive my car on extremely bumpy road (not even a road just stones).

 

Nope I have not changed my AC filter. AC/heater working perfectly no issue with working of cooling and heating system.
yes there is a little damage underside of car just behind front wheel mud flap, reinforced area. I will post the picture later

 

Yes i will first replace the cabin air filter, all AC buttons are working normally. i will inspect the intake ducts and will post here the results.

below are the two pictures of underneath damage to car, but i don't think so they are the reason

 

I have already checked this area, its okay not enough damage to cause rattle or dust ingress. i will check the cabin filter on weekend. will update after