In training mode I like to create markers for positions I made a mistake in. That way I can review them in the repertoire mode after the training. How can I remove these markers afterwards, so that if I create new markers in the next training I don't have to go through my markers of earlier training sessions?

Click on the Position tab to the right of the Repertoire tab. The Mark As box should show "Training." Click the dropdown arrow and change to "None."

You have to do the same thing when you do Run Against Games. CPT then marks positions as Novelty. After reviewing I change Novelty to None.