I think your puppy has you in a perfect recall!!
The puppy whines and you appear and give him a cuddle, you have taught him that however long he cries you will appear and cuddle him!!! Perfect recall by the puppy!! LOL
We use a crate with Logan, he has slept through from about 12 weeks of age. Our routine was crate in the bedroom for the first couple of weeks and set the alarm every 3 hours to take him out to the toilet, we used to take him outside but not put the light on or talk to him only to praise him when he went to the loo. Then straight back in his crate, he would whimper for a few seconds but we just said 'bedtime now' and he was reassured just by hearing us and went back to sleep everytime. After two weeks in our bedroom we moved his crate to the lounge and still got up 3 hourly for toilet breaks. He is now 17 weeks old and as soon as we say bedtime he goes in his crate and waits for his bonio and now sleeps through without the need for toilet breaks until 6.30 am, (we go to bed around 10.30pm). He has never messed or wet in his crate and he is now left for 5 hours a day some days in it while i go to work.
I hope this helps, not to say this routine works for every dog but this is my 4th puppy i have done this with and it has worked for all of them.

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