Preheat oven and cook beef: Preheat oven to 425°F. Heat a large (5-quart) heavy pot or Dutch oven over high. Cook beef, breaking up meat with a spoon, until no longer pink, 4 to 5 minutes. Add onion and garlic; cook until softened, about 4 minutes.
Add thyme, ketchup, and flour, then vegetables and water; cook briefly until thickened: Add thyme, ketchup, and flour; stir until combined. Add ½ cup water and vegetables. Cook until vegetables are warmed through and liquid has thickened, about 3 minutes. Season with salt and pepper.
Assemble pie: Spoon beef mixture into a 2-quart baking dish. Spread potatoes evenly over beef; using a fork, decorate potatoes with lines and peaks.
Bake: Place dish on a rimmed baking sheet, and bake until potatoes are lightly browned, 10 to 15 minutes. Serve.
