The game has both -- elements which only spawn because of certain actions you take, and also elements which don't spawn because of a bug.
In your case, you ran into a bug. Once you cross the bridge beyond the forest of traps, passing the non-functional railcar, there are a number of interactable elements found on the railroad tracks: ropes; the severed legs; a blood trail leading down a trail (with a body sans legs); a bloody rock; a gas can; a pile of rocks. The fact that you saw "nothing of interest" is telling.
The crankshaft, similarly, should be there immediately. It is a bit out of the way, however, so I wouldn't be too surprised if you had just overlooked it.
I started a new game and sprinted from the initial start point through to the severed legs and found them immediately, which confirms what I've said above. I also sprinted down to the shoreline and found the crankshaft.
The elements which spawn due to actions you take generally revolve around Ethan's stories. As you solve some of the side puzzles, you find more of Ethan's stories -- usually in the 'alternate dimension'. Once you read his stories, you'll be brought back to reality, which has usually changed minutely in the form of additional things to interact with (notes, news clippings, magazines, these sorts of things, usually.)
Here's some examples:
- After finding the spaceman and getting on the spaceship, you read Ethan's story and then find yourself back in the proper reality in a small shed that hadn't previously been there. In the shed is the same story you read, plus a defaced Sci-Fi fiction magazine.
- When you get to the mine, you'll notice the mine entrance is padlocked. After solving the riddle in the maze and reading Ethan's story about the cursed miner, you'll be teleported out of the mine and find a bunch of papers on the ground along with Ethan's story -- including a letter from the US Patent & Trademark Office, and a note from Missy to Dale.
These are the sorts of items that spawn because of your actions; they're generally atmospheric and story enrichment items, not anything which is critical to the gameplay itself.
That all being said, there is only one place that I've found where something hasn't spawned because of a bug, and which doesn't spawn at all during the play through. This is specific to the hidden item you have to find in order to get the secret "Unfinished Story" achievement:
To get this achievement, you have to find the sniper rifle. To do this, you need to first find the pine cone/grenade in the forest on the left of the rail tracks, just past the severed legs area. Once you reach the bridge, you need to throw the grenade into the water from the third viewing area on the bridge. Then later, once you get into the dam control room after solving Dale's murder, you can find a dead scuba diver with a sniper rifle washed up on shore on the beach just past the dam control building. However, sometimes the dead scuba diver doesn't spawn at all.
This is actually something that happened on my first play-through, and nothing I did could cause the missing item to spawn. I had to start a new playthrough to get it to spawn properly and award the achievement.