I downloaded the route and I have faulty dependencies in the form of the Tb Forest and faulty dependencies on the Rusty G16a Locomotive and Tender and I must be missing some gravel by the looks of the photo here.
Couple of things here.
Ensure you've got all the dependencies, and that nothing is open for edit. If anything is already installed and you install the same asset, they will be left open for edit. You need to choose the open for edit filter highlight them, and then choose revert to original.
This will close up all the assets that are open for edit and that should work.
The tree bush issue may be related, but it may also have to do with the season. The asset may not have a winter season, and for some reason TB assets disappear. Try adjusting your season to summer by editing the environment and changing the date to July and see if that works.