Haven't seen this on our Clarity, but on a Toyota Tacoma Truck that I purchased used from a private party, I found exactly this problem when doing my first maintenance: lots of mouse nest debris on top of the cabin filter, including dried natural vegetation, chewed pleats, and most concerning, black expanded foam presumably from somewhere on the vehicle. "My bad" for neglecting to check that filter before purchasing, but in reading about other's experiences, obviously I got, because there was no sign of continuing mice presence, nor did I find any signs of chewed wire insulation. I did have to drop the motor assembly to clean the blower wheel as part of changing the air filter, because lots of debris was scraped off and dropped into the blower wheel when the old filter was pulled out, but that was a minor inconvenience that didn't take long to fix.
A Toyota service manager I asked about the foam replied that it was probably material used on the perimeter of the cabin air intake flap which responds to the fresh or recirc. climate control setting. He thought there was little downside to leaving that damage unrepaired, fortunately, since the cost to disassemble everything needed to replace that foam seal was out of sight! He also said the cabin air intake is the most frequent point of access for mice to get into the air ducts. His suggestion on how to avoid mice cabin incursion was pretty much what other posters in this thread have said: use peppermint oil as a deterrent (especially applicable to avoid bringing new critters home from other places), and set regular traps in the vicinity of where the vehicle is normally parked. I didn't have any peppermint spray or liquid, so dropped mini Altoids into the filter pleats. Don't know if that was really effective, especially since the new filter had the activated charcoal feature to absorb smells. At least I have never seen signs of mice since the purchase, but maybe that's just because there have never been mice in our garage (and knock on wood that doesn't change!).
But his advice did get me thinking - if the initial access is "typically" through a vehicle's external air intake (wherever it is located, and on whatever model car), wouldn't it help to always set the climate control to "recirc." (to close the flap) before parking the car every time? Even if the flap was plastic and vulnerable to chewing, being closed might offer some deterrence advantage. Of course this would require developing a new habit, but would probably be easier than locating the cabin air intake and somehow fashioning a porous non chewable barrier that stays put and does not interfere with flap operation.
It also seems it would be fairly easy for manufacturers of modern cars to use a chew proof sheet metal flap on the air intake control (aluminum, maybe) and even to have it automatically close on shut down (restoring the prior setting at next use). While this is not the worst problem in the world of cars, if you or your significant other dislikes rodents as much as mine does, than this feature alone (with creative marketing) would probably sell a lot of cars!