It's not a clear contradiction; it's one of only two cases that are arguable (the other one being NATO bombing of Serbia during the dissolution of Yugoslavia).

It's noted that it's not clear how much the atomic bombings influenced the decision to surrender, versus the near-simultaneous declaration of war by the USSR on Japan. Furthermore, by the time Japan surrendered, it was clear that Japan had already thoroughly lost. Recall that similar bombing campaigns against the UK (Battle of Britain) and Germany utter failed to bring those nations any closer to surrender.

In any case, compared to the actual theorists like Giulio Douhet who were, before World War II, arguing that attacking cities would cause the will of the nations to collapse before they fully mobilized, the actual results fell far short of the theorists.