Lemon pie filling may be runny due to the custard not being set. Lemon meringue filling can be thickened either by using corn starch (which relies on heat to activate it) or by using egg yolks and condensed milk (like this recipe). If you're using corn starch, the filling is runny because it was not heated long enough on the stove. If runny and using egg yolks, it's because it wasn't baked long enough. To verify the pie is set after baking, gently jiggle the sides of the pie to see if the center of the pie slightly jiggles but is solid when touched.