Preheat the oven to 325°F with a rack in the center.
Place a wire rack on top of a large baking sheet, then place 12 nonstick baking cups on top.
Lightly grease the cups with nonstick spray.
Divide the mix-ins evenly among the 12 cups; aim for about 1 tablespoon of mix-ins per muffin cup for best results.
In a blender, combine the cottage cheese, eggs, salt, and pepper.
Blend the mixture in short bursts until the cottage cheese becomes slightly smoother, about 30 to 60 seconds total.
Pour the egg mixture over the fillings in each muffin cup; each cup will be nearly full.
Bake the egg bites for 20 to 22 minutes, until set in the centers.
Remove from the oven and let cool for a few minutes before unmolding and serving.