What causes a small and large vapor leak on a 2000 Chrysler 300M, and
should the repair be covered by the emissions warranty? (the car is
still under warranty, but if it's not a factory defect, it won't be
covered.

vapour leak, 
 poss vapour smells"petrol" causes could be a split or damaged fuel
pipe or line somewhere on the vehicle.
 poss carbon monoxide  smells can be a blowing muffler or incorectley
sealed door or boot rubber trims.
 your warrenty will cover for manafacture defects only and if the leak
came from say driving over somthing that splits the line it would not
cover this.