Good point, especially when the problem is often subdependency of a subdependency of a dependency. Just to clarify, a big part of learning to play Trainz is learning how to use and interpret content manager. Not to be insulting, but rather than assume you already know this;
In that pic one route is showing a missing icon, the other is showing faulty, what you have to do is dive down through the lists of dependencies and sub dependencies to locate the actual culprit before you can start troubleshooting how to fix it. Example a session shows as faulty so it's not in the menu in game, find the session and it has a faulty puzzle piece icon. List dependencies, got a consist showing faulty. List dependencies for that, a boxcar is faulty. Except the boxcar itself is fine, the problem is one of the commodity loads associated with that boxcar is what's actually faulty, and it affects the whole chain up to the top.

In that pic one route is showing a missing icon, the other is showing faulty, what you have to do is dive down through the lists of dependencies and sub dependencies to locate the actual culprit before you can start troubleshooting how to fix it. Example a session shows as faulty so it's not in the menu in game, find the session and it has a faulty puzzle piece icon. List dependencies, got a consist showing faulty. List dependencies for that, a boxcar is faulty. Except the boxcar itself is fine, the problem is one of the commodity loads associated with that boxcar is what's actually faulty, and it affects the whole chain up to the top.