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It has to be the first thing you do in the morning after the new day started. If an even triggers before you can get to that missions spot. Start a new day and go there right away. While the game does not officially tell you. There is a Morning, Day and Night cycle. Morning ends immediately after doing one event or harvesting right after getting out of bed

You have to continue the story a little further. When you first unlock the sex scene she can't get pregnant right away even though it shows the fertility animation. The game will tell you she CAN get pregnant close to the end of chapter 3 I want to say. Just keep doing all the side stuff too.