Preheat the oven to 375°F.
Cook pasta shells according to package directions. Drain well and set aside.
Heat the oil in a non-stick pan on medium heat. Sauté the onion and garlic until golden brown.
In a bowl mix the ground beef, onion, garlic, milk, breadcrumbs, Worcestershire sauce, fontina, salt and pepper until fully combined.
Spoon the beef mixture into the cooked pasta shells.
Place the broth, cream, stuffed shells, thyme, and mushrooms in a baking dish. Cover with foil and bake in the oven to an internal temperature of 160°F using a thermometer, about 20 minutes. Then remove from the oven, using a slotted spoon remove the shells from the baking dish.
Pour the remaining liquid and contents into a pan over medium heat. Add the butter and bring to a simmer until the sauce becomes thick and smooth. Taste and season with salt if needed. Then remove the thyme sprigs.
Spoon the sauce and mushrooms over the shells. Garnish with parmesan and red pepper flakes. Serve with dinner rolls.