Some more details would be helpful. Has the vehicle been exposed to road salt or near the ocean? Is it regularly washed and or waxed?
Regardless, I would address the rust now. There are products such as rust converter.
I am about two miles from the ocean, park inside a carport, and salt stains will appear on my car after one day because there is salt in the air. I use a high pressure hose attachment as a regular hose spray will not fully remove the salt stains. I undercoated the vehicle when it was brand new.
The likely solution for you is to use Rust converter from Home Depot, then paint to match. Unless you can get it covered under warranty.