It is taking me longer to come up with a title than write this.
What struck me most about this film were the many small specific examples that helped to create a counter cinema. The disjointed narrative and tracking shots are two broad examples, but Vagabond nudges our mind away from the classic road film in more subtle ways as well. In the film both agriculture and urban enviroments are portrayed as prisons. Shots composed through metal spikes, bars, or fences are frequent. There are also many shots of the trees as bars against the sky. In the opening scene as she is coming out of the water on the beach the frame is sectioned by fence posts. The road is also the thing that dictates what she should do, and the first thing she ignores, when she walks past a stop (no trespassing?) sign. This representation of the road not conquering nature, but rather as a prison created by it is the exception in road film.
Another exception found in this movie that is rare in films focused in the male gaze is that there were no simulated rape scenes. Simulated rape scenes are often shot to illicit a sexual response despite of the level of horror in the act. The fact that you didn't see her raped, but were still shown the end of one and the begining of anotherwas my most appreciated interruption of the male gaze.
other examples:
There is often a male gaze where the audience is more aware we are looking through a males eyes. In these shots we often see Mona reflected in a mirror, or through glass, giving the male gaze less power than it would normally have.
Mona starts out rolling her own cigarettes, shaping herself what is often considered a phallic object.
Shots are often comprised not around Mona's body, but rather on the effect her body has had. You may not see her, but you know what her agency has created.