Debugger rendering problem

I am trying to develop a robot simulator for machine learning. Sometimes, when everything is working fine I have some results like this:
This is a sample that my simulator saves to the hard drive.
Some other times, specially after I wrote some code with bugs, I find that the simulator is rendering images like this:

The problem is with the shadows that appear in those cases. That shadows can look very different to my deep learning algorithm, even I find that the new palette looks different too.
This can happen with different bugs, not necessarily related to the render pipeline. But if this is not a general bug from Unity, What is it then? Does it have any solution?
I can work with some bugs in my code. But I can’t work with this problem. In this instance, the only thing that the console is complaining about is that It can’t find the NavMesh. I don’t know how this could be related because the agent is still able to move.

An update on the subject
I work my simulations with 4 scenarios. When I finish with one, another instance is loaded until the maximum amount of repetitions. Then I load the next scene.
Apparently, the scenarios when back to normal when I started the simulation directly from the scenario, skipping the main menu. This worked well only for those that I tried independently. Those that I left intact retained the change in aspect. Could this be a cache problem?