It happens because the lids have shrunk during cooking. Pastry that has been chilled for 20-30 minutes before rolling will relax and shrink less. Short, light strokes are also important when rolling out pastry as pushing the rolling pin heavily will stretch the pastry and it will shrink during baking.
Pies made in deep oval dishes are always made with a single crust as the shape makes it difficult to line the dish properly. But there must be sufficient filling to mound above the rim of the dish and support the pastry lid.