Peel and dice the apples and place them in a large bowl. Toss the diced apples with the flour, sugar, cinnamon, nutmeg and salt.
Heat a large pan over medium heat and melt the butter. Add the apples and cook for 10 minutes over medium-low heat, allowing the sugar to caramelize. Add the water and cover the pan with a lid. Cook the apples until soft and tender, about 20 minutes, stirring every couple of minutes. If caramel thickens too quickly or begins to burn, add more water. Remove the apples from heat and let cool at room temperature.
Preheat your oven to 350°F. Unroll the pre-made pie crust onto a baking sheet. Pierce the crust with a fork and bake in the preheated oven until edges turn golden brown. Remove from oven, cool, then break into small bite-sized pieces.
Prepare the whipped cream before serving. Place the heavy cream, confectioner's sugar and vanilla extract into a mixer bowl and whisk until peaks form.
To assemble the dessert, spoon generous amounts of the caramel apple mixture into glass or plastic cups, followed by the pie crust pieces and top with whipped cream. Refrigerate if not serving immediately.