You didn't throw away the pills.

You made good on your promise to Saeko, which was to claim her on her marital bed all week long. As you fucked her throughout the week, you drew her attention to the pills in the waste basket from time to time. You tell her that the box was there, in case she's worried about what you're doing to her. However, you added that for the pills to be effective, she has to take it within 72 hours after you seed her womb.