Just let the discomfort be
Sometimes, while practicing spirituality, uncomfortable feelings come up. When I first realized that most thoughts arise automatically, I felt some discomfort. I wanted that feeling to go away, but the more I tried to push it away, the worse it got. The same thing happened when I tried a different meditation technique from the one I had been using.
I came across a Buddhist teaching that suggested not pushing away the thoughts or discomfort when they come up. I tried that, and strangely, it did fade on its own without any effort from my side.