The bubbling phase can be prevented from occurring by setting the event's bubbles property to false when creating a custom event, or by certain events that don't bubble by default (like focus/blur). The capturing and target phases always occur and cannot be prevented by default. However, event propagation through any phase can be stopped programmatically using stopPropagation() or stopImmediatePropagation(). Understanding which events bubble by default is crucial for proper event handling.