Preheat the oven to 375. Place cupcake liners into 12 cups of a standard sized muffin/cupcake tin and place a Nilla wafer in each liner.
In a large bowl, combine the cream cheese, yogurt, 1/3 cup of sugar, egg, vanilla extract, lemon juice and cinnamon and mix together using an electric mixer until smooth and well combined. Spoon the mixture evenly on top of the wafers into the prepared liners and spread flat with a spatula or the back or a spoon. Bake for 15-16 minutes and remove from oven to cool. Once the cheesecake cups have cooled to room temperature, transfer the cheesecake cups to the refrigerator and chill for at least one hour.
In a small saucepan, bring the butter to medium heat until melted. Add the chopped apples and stir to coat. Cook uncovered for 4-5 minutes, stirring occasionally. In a small dish, combine the sugar, cornstarch and cinnamon and stir together. Pour the sugar mixture and the water into the pot with the apples and stir to combine. Cover the saucepan and reduce heat to low. Simmer for 3-4 minutes until the mixture is thick and apples are tender.
Top each cheesecake cup with about a tablespoon of apple topping and serve.