Puppies could be squeaky and whining ... due to boredom, seperation Anxiety, lack of training, Pain or medical problems, Bloating or if it has some Digestive issues...If u think Your dog stomach hurts...Try changing her to higher quality, bland food that it can easily digest..if whining eases during this time then u can assume ..diet is causing the issue...
Encourage them for lot of excercise, Kindly hire a dog trainer to focus on whining problem...Puppies whine more than adult dogs, coz they miss their littermates, mother...and they want your attention...