Melt the butterscotch pieces with 1 tablespoon of the milk in a bowl over simmering water in a saucepan; stir until smooth. Whisk in the cream cheese until smooth. Evenly divide among phyllo cups, using about 1 teaspoon filling per cup. Refrigerate until chilled.
Melt the chocolate pieces with the remaining 1 tablespoon milk in a clean bowl over simmering water in a saucepan. Spoon into a pastry bag fitted with a medium-large round tip. Pipe a large dot of chocolate onto top of the butterscotch filling in each phyllo cup. Top each cup with a pecan half, pressing the pecan into the chocolate.
Refrigerate until the chocolate is relatively firm to the touch. Remove the cups from the refrigerator 10 to 15 minutes before serving. Makes 30 mini cups.