If the saddle rails were bent so the distance between their ends had reduced then less effort would be needed to pull the saddle off the rails. We see this often enough. usually from jumping off curbs and such, or a really big rider getting a bit bouncy. A fender dent could happen any time but maybe only be noticed later. I can believe a bike moving around in a trunk could easily cause a fender dent. And being plastic you might not hear much impact noise. As to the bike being in the same place in the trunk... the last motion the car went through each time before you open the trunk was the car coming to a stop. Of course the bike would be in that position each time you looked and the tendency is to put the bike in the trunk the same way you saw it when you got it out. As to the tire did any one do an examination of the tube's failure? A prick hole, a tear, a star burst hole, inside or outside the tube? We see many tubes that have been holed by grit left inside the tire during installation. Also a piece of glass/flint can wedge into and through the casing then get ejected when the tire goes soft and flexes a lot. If your tires have a tread pattern to them then pieces of glass can get trapped within the tread slots and continue to get pushed deeper into the tire casing with each revolution. periodically looking for bits in the tire casing and removal if seen can prevent many flats otherwise in your future. Andy.