For the crust: Preheat the oven to 350 degrees F. Line two 12-cup standard muffin tins with paper liners.
Combine the graham cracker crumbs, granulated sugar, cinnamon and butter in a small bowl. Drop a heaping tablespoon of graham cracker mixture into each muffin cup. Press to create a firm layer of crust on the bottom. Bake 7 minutes. Set aside to cool completely.
For the cupcakes: Combine the flour, baking powder, baking soda and salt in a medium bowl.
Using a hand mixer or stand mixer, cream the butter and granulated sugar together until fluffy, 2 to 3 minutes. Add the eggs, one at a time, scraping down the bowl between additions. Beat in the vanilla.
Whisk together the sour cream and the milk. Add the flour mixture and milk mixture in three additions, alternating between wet and dry ingredients and starting and ending with flour mixture. Beat just until well combined, taking care not to overmix.
For the filling: Beat the cream cheese and granulated sugar in a bowl with an electric mixer at medium speed until light and fluffy, about 3 minutes. Beat in the egg just until combined. Spoon the filling into a pastry bag fitted with a medium-size plain tip (Ateco 800). Insert the tip into the top of each cupcake batter and squeeze the filling until the batter rises to fill each cup about three-quarters of the way up the side of the tin.
Bake until lightly golden and a toothpick inserted about 3/4 inch from the edge of the cupcakes comes out clean, 18 to 20 minutes. Cool the cupcakes in the tins on a rack for 10 minutes, and then remove from the tins and cool completely.
For the frosting: Using an electric or stand mixer, beat the cream cheese and butter together at medium speed until fluffy, about 2 minutes. Scrape down the sides of the bowl. Beat in the sour cream and lemon juice. On low speed, gradually add the confectioners' sugar and beat until well combined.
Frost the cupcakes as desired. Garnish with graham cracker pieces.