Place the beef in a bowl and sprinkle with 1 teaspoon of dried ground chipotle chile, tossing to coat.
In a Dutch oven, brown the beef in 1 tablespoon of hot oil over medium-high heat.
Stir occasionally, and this should take about 10 minutes.
Remove the beef with a slotted spoon.
Add the onion and green bell pepper to the Dutch oven, and cook, stirring occasionally, for 3 minutes.
Return the beef to the Dutch oven, and stir in the remaining 1 teaspoon of dried ground chipotle chile, butternut squash, and the next 4 ingredients.
Bring the mixture to a boil.
Cover the pot, reduce the heat, and simmer, stirring occasionally, for 30 minutes.
Cook flour in the remaining 1 tablespoon of hot oil in a small skillet over medium heat, stirring constantly with a wooden spoon, for 5 minutes or until it turns golden.