I have owned one of these trucks for 37 years and have seen many with that same damage as well. What it comes down to is of course the door was opened too far, it is simple as that. Trucks are usually used a little rougher than cars and likely it happens because the truck is being used for work and some person jumping out to tend to a downed fence or delivery of firewood or something jumped the gun and opened the door before the truck came to a complete stop. OR, the simple fact that the original door latches SUCK big time. I know I had a friend swing out on the door as I went around a corner back in high School! Luckily the window was down and he hung on and didn't fall out of the truck. But that is likely how these damaged cowls occurred.
How can you stop it, well, don't swing the door open too far.
But honestly, outside of bending the hinges so they don't allow the door to open quite as far so if it does get "sprung" a little it won't hit. OR install a "check strap" device.
I personally wouldn't worry about it, just don't treat your truck like a truck.
But give it a good look see and check to see if the doors hinges may be bent from being sprung. If your door has hit the cowl before there is a good chance your hinges and or mounting points are bent a little.
Here is a "basics" I put together on the subject of sprung doors.
Click here for the "Basics of Basics" Sprung doors.