Obviously your puppy knows that she is suppose to poop on the pads.... in the pen... cause she goes on the outside of it when she has to go! ( At least you know that she knows what the pads are for!) Maybe you could place a pad on the outside of the pen, when you are home,... just for these "emergency moments" and then gradually move the pad to the area that you want it to be.... maybe by the door? This may help!
Our little male (Seymour) gets up during the night... every-night. He either needs to get a drink or use the bathroom....... or sometimes one of each. I really think it is the individual dog. Our female (Shelby) never needs to wake up and she is the last one out of bed in the morning. My suggestion is only a small amount of water in the evening ..... maybe try sleeping in the day pen instead of the crate at night. She may feel more at "home" in the pen! Could you move the daypen to the bedroom in the evening?
Eventually she will settle into a routine. You sound like a great owner who cares enough to ask questions and wants to do what is the best for a furkid! Good Luck! Merry Christmas to your family and Matilda!
