I feel you Trail Runner614.  It only takes a poorly placed spider in a boot to ruin an otherwise spectacular day on the trail. 

I too keep my foot wear inside the 1.5 person tent I backpack with, along with my pack. Generally, the only thing I leave out over night would be kitchen gear, stove and perhaps fuel, no food reminisce of course.  Bear or cat country, right? Another quick way to ruin a trip is to attract a bear or cat. 

I have found evidence of small rodents and insects that have crawled inside the vestibule to investigate things I have left outside there. I once had a rodent naw at my shoelace, I’m guessing because of the sweets or jerky scent/flavor I had on my fingers?

Ultimately, when on a multi-day trip, I don’t wait for the wild or Mother Nature to surprise me, I hope I’ve done my due diligence to be prepared, so as to pass thru her beauty like I was never there.  

Good luck. Be safe. Stay healthy. Keep fresh.