Collision coverage is intended to cover things that your vehicle strikes while Comprehensive coverage is intended to cover things that strike your vehicle. Comprehensive is supposed to cover un-excluded loss other than collision or overturn.
It can be difficult to determine which occurrences are covered by collision and which is covered by "other than collision" (comprehensive) when discussing objects.
Your insurance company will ultimately decide if the damage caused by your vehicle running over a piece of highway debris will be covered by the collision or comprehensive part of your physical damage insurance coverage.
Once you place a claim with your insurance provider the claims adjuster will investigate the incident and damage sustained to determine what they decide this type of accident would fall under. If you caught a piece of metal, wood, debris of another type that flew up off the highway then would likely be considered comprehensive and not collision since the object hit your vehicle.
Your insurance adjuster should let you know if this as a comprehensive or a collision claim and thus which deductible is due.