I had a similar problem with late 2012 rMBP starting from El Captain - often after a touchpad click anywhere a rolling ball appeared for a few seconds before al

I had a similar problem with late 2012 rMBP starting from El Captain - often after a touchpad click anywhere a rolling ball appeared for a few seconds before allowing to do anything, which was making it unusable. Then logic board died. So it might be a symptom your MBP is moving towards end of life or to "hot oven maintenance" checkpoint.