Peel, core, and dice the apples into 1/2-inch pieces.
Melt 2 tbsp butter in a large skillet over medium heat.
Add apples, brown sugar, cinnamon, nutmeg, and a pinch of salt; cook until tender, 8–10 minutes.
Stir in lemon juice and vanilla; remove from heat and let cool 5 minutes.
Combine graham crumbs, melted butter, brown sugar, and salt until evenly moistened.
Toast the crumb mixture in a dry skillet over medium heat, stirring, 3–4 minutes; cool briefly.
Warm the caramel sauce until pourable in a microwave or small saucepan.
Spoon a layer of crumbs into serving cups and press lightly.
Divide the warm apples among cups and drizzle with caramel.
Top with whipped cream and pecans, then serve right away or chill 10 minutes.