Yes so true. I know I have practiced 'Mindfulness' over the years and have learned Cognitive Behavioral Theory from research. And one of the principles that has resonated with me in treating my Clinical OCD is similar to what you describe.
That is my Mind will wander off and give out a false alarm that something is wrong. There is no way to stop this from happening.It's just physical mechanisms and neuron firing in my brain.
But the only thing I can control is my response to it which involves doing an activity of sorts that I enjoy. And eventually through time the negative thoughts will subside.
But to try to "out think" the negative thoughts or "think it through" and forcefully get rid of the negativity will only make it that much worse !!