Heat the oven to 350 °F and place 24 cupcake liners in a muffin tin. Have the pan ready before mixing so the crust can go straight into the liners.
Stir the graham cracker crumbs, melted butter, and sugar together in a large bowl, then divide the mixture among the liners and press it firmly into the bottoms. The crumbs should form an even, compact layer with no loose patches around the edges.
Bake the crusts for 5 minutes, then leave them in the muffin tin until completely cool. The crusts will look set and smell lightly buttery rather than wet or loose.
Use a hand mixer to beat the room-temperature cream cheese until light and smooth, then blend in the sugar. The mixture should look fluffy and creamy with no visible white lumps.
Whisk the eggs in a small bowl, then fold them into the cream cheese with a silicone spatula just until combined; gently mix in the lemon juice and vanilla extract. Stop as soon as the batter looks uniform to avoid adding excess air.
Fill each cooled crust about 2/3 full with the cheesecake batter. Leave room at the top so the filling can rise gently without spilling over the liners.
Bake for 15 minutes. The edges should appear set while the centers still give a slight, gentle jiggle when the pan is nudged.
Cool the cupcakes in the pan, spoon cherry pie filling over each one, and chill until completely cooled. A shallow center indentation is normal and neatly holds the cherry topping.