Most of the major quest steps let you take breaks between them; I know for sure I took a pretty long break after sparring with Hans to train with Bernard, I took a pretty massive one before scouting Pribyslavitz, and I took a pretty long one after first encountering Ulrich (both after I caught up to him in the horse chase on my first run and after he asks to meet by the pond when he outran me in my second run).

Most of the time you can assume that you're on a break; I think the only time I got reprimanded was when Bernard and the troops were ready to go to Neuhof to investigate the scene and I didn't go directly to Bernard after the previous cutscene.