As far as I can determine, there is not a huge difference between the two terms. As a very general rule, "stuffed" refers to a non-dessert food items. A turkey can be stuffed with dressing, cannelloni noodles stuffed with ground sausage, mushroom caps stuffed with crabmeat, etc. "Filled" usually describes a dessert item, such as a cream-filled pastry, or a pie with custard filling.
Student or Learner