I had a similar problem, though they never ran up and down my legs
. The next summer the car smelled a little funny. I looked under the seats, in the dash, trunk, etc...
Finally found two dead mice in the headliner!
I had to replace it because of all the rat poison, sunflower seeds, and mouse s#$t. I found one nest right up by the sun visors and one in the passenger sail panel.
This year, as suggested by Donotchallengeher, I placed irish spring soap bars in the trunk, under seats, on the package shelf, and in the air ducts. So far no problems.
That 'fresh' scent is just tooooo much for rodents I guess