A utilitarian weights up consequences for all actions. If alternatives on calculation produce the same utility value, they are equally good. Conflicting duties, however, call on me to take logically or physically incompatible action. In crude Kantian terms acting on one duty but not on the other is itself unethical - a breach of duty. Thus rather than unwaveringly standing on principle we take steps to qualify our maxims to avoid unacceptable outcomes.
Deontological ethics is strongest where utilitarianism is weakest.
In an ethics of duty, the ends can never justify the means. Individual human rights are acknowledged and inviolable. We need not consider the satisfaction of harmful desires in our moral deliberations.