FYI I've suffered from this a lot. They don't appear necessarily on the beat but can pop up in random places. It's PITA to try to use the AS when there are "phantom transient markers" very very close to actual ones (so close you can't see them unless you zoom all the way in) as they mess with you when you try to move transients. And when you select "user markers" you can turn them inactive but can't delete them (only a random part of them gets actually deleted and the rest stay there).