Line an 8x8 inch pan with parchment paper or foil. Spray with baking spray and set aside.
In a heavy-bottomed pan set over low heat, combine the chocolate chips, butterscotch chips, and sweetened condensed milk. Stir until melted and completely smooth and combined.
Remove from heat. Stir in vanilla extract. Pour the chocolate mixture into the prepared pan and spread evenly. Sprinkle flaked sea salt over the top. Let cool completely at room temperature. Remove from pan and cut into 36 1-inch squares. Store in an airtight container.