Preheat the oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone baking mats and set aside.
In a medium bowl whisk together the flour, cocoa powder, baking soda and salt until evenly combined. Set the dry mix aside.
In a large mixing bowl, beat the softened butter and granulated sugar with an electric mixer on medium-high until very light and fluffy, about 3 minutes. Scrape the bowl down as needed.
Add the egg, vanilla, apple cider vinegar and red food coloring to the creamed butter and mix on medium speed until the color is uniform and the mixture is smooth.
Fold the dry ingredients into the wet mixture with a spatula or mix on low just until no streaks of flour remain. Avoid overmixing to keep cookies tender.
Chill the dough in the refrigerator for 15 minutes — this firms the dough for neater shaping and a slightly thicker cookie.
Roll dough into 1-inch balls (about 1 tablespoon each) and place them 1 1/2 inches apart on the prepared sheets. Use the back of a teaspoon or your thumb to press a shallow well into the center of each ball, about halfway through but not to the bottom.
Bake one sheet at a time on the middle rack until the edges are set and the centers look just slightly soft, 9–11 minutes. Rotate the pan halfway through if your oven runs hot.
Remove the cookies from the oven and immediately press a white chocolate wafer into the indentation of each cookie. Let the cookies cool on the baking sheet for 4–5 minutes so the wafers soften and adhere, then transfer them to a wire rack to finish cooling.
If any wafers don’t melt smooth into the centers, microwave a few extra wafers in 10-second bursts until soft and spoon a small amount into the wells to finish.
Cool completely before storing. Cookies keep in an airtight container at room temperature for up to 4 days or freeze for longer storage.