@Slimboyfat: there is an easy answer and it is called the scientific method. Yes, if you’re sampling one instance of an event, you will draw the wrong conclusion. Thus scientists will attempt to sample multiple independent and dependent events in different locations to try to deduce a theory.
In your bus example, scientists wouldn’t just look and note the event, they would find other bus stops and see if the same occurs there too. Then they would attempt to control the variables of the experiment by withholding the bus or withholding the people or moving the bus stop and seeing what happens. You can kind of see in that case that if you withhold the people, the bus still shows up, thus you can conclude it wasn’t the people causing the bus to show up.
Likewise with the brain, what you’re looking for is explained through DTI analysis of the brain, you’re basically sticking a bunch of people in an MRI and see whether the blood flow preceded or succeeded an event. And you can confirm it in the other direction as well by activating the area through for example electrodes or magnets you can activate feelings and thoughts.
The brain is very complex but healthy brains are relatively well understood at this point. We don’t know a lot about the specifics of consciousness or memory, but we know where those things happen. We have to continue probing and changing variables, the biggest problem is that humans are a valuable commodity, unlike the Nazis or China you can’t just kill or alter a ton of people in the pursuit of knowledge.