Preheat an oven to 350 degrees F (175 degrees C). Place phyllo cups onto a baking sheet.
Stir together cream cheese, Cheddar cheese, jalapenos, and hot sauce in a bowl. Spoon mixture into phyllo cups. Sprinkle bacon bits on top. Bake in preheated oven until golden brown, about 15 to 20 minutes. Serve warm.