I am noticing Position Markers in many of my tracks which I did not place myself. I mostly notice them in podcasts when I go back to listen to them again after listening through and stopping at the end with the "Stop Playing After This Track" option selected. It is not only podcasts where I notice the markers, but I use "Stop Playing After This Track" much less frequently on local collection songs. I believe that "Stop Playing After This Track" is creating a Position Marker at the end of the track every time when play is stopped.
This is not a bug, but a feature. Position markers are needed to be able to resume play on start, even if you do not use this feature.