Rules are always created for a higher purpose. Sometimes, keeping that higher purpose requires breaking the rules.
Rules are specific descriptions of behavior in a specific situation. The problem is that situations differ one from another, and sometimes the behavior more true to the principle will actually require you to break the rule. This might seem hard to believe for anyone who hasn’t had extensive experience in highly regimented situations, such as the military.
There’s a time and place where the spirit of the law requires you to violate the letter of the law. While it is true that the major applicability of rules is why they are attractive in the first place, anyone who is serious about living a certain character quality is going to run up against a situation like this sooner or later. While the occasional need to break the rules can be abused to justify poor choices, it is absolutely necessary to learn to apply them with prudence, honesty, and wisdom if you really want to fully embody a character quality.
Conflict can appear at the principle and quality levels, too. For example, you may encounter situations where you find a conflict between being just and merciful, patient and proactive, calm and assertive, etc.
One of the strengths of the hierarchy of character, quality, principle, rule is that the parent category gives overriding guidance to the subordinate one. When you find yourself questioning whether a rule, principle, or quality should be broken, do what aligns best with your purpose and the remaining categories.