Listen first, do not silence
Two in the morning. The puppy whines. Five minutes later the whining turns into barking, and nobody in the house is asleep.
At a moment like that a person wants one thing - for the noise to stop. That is entirely natural and nothing to be ashamed of.
But the same sound can mean very different things. Dissatisfaction. Tiredness. Needing the toilet. Over-arousal before sleep. Fear. Or genuine separation distress, which is no longer a question of habit.
So barking is not a diagnosis. It is information that something in the present situation is hard for the dog. The question is what exactly.

What a crate is actually for
A crate or a pen can be genuinely valuable. It keeps a puppy safe from danger when we cannot watch him, gives him a predictable place to sleep and makes travel and veterinary procedures far easier.
But all these benefits come with one condition: the space has to be associated with safety for the dog.
A crate should not be a punishment. It should not be a way of isolating an “inconvenient” dog. And it certainly should not be an attempt to force him to learn to be alone.
One uncomfortable truth is worth remembering: a quiet dog does not necessarily feel safe. Sometimes he has simply stopped believing that his signals will be heard. From the outside that looks like a victory.
Protest and panic are not the same thing
Brief dissatisfaction with a boundary looks different from mounting distress - and that difference is worth seeing.
Brief dissatisfaction with a boundary looks different from mounting distress - and that difference is worth seeing.
The whole picture matters in assessing this: tension in the body, whether the dog can take food, whether he can catch his breath, lie down, be distracted, how intense the behaviour is and - most importantly - whether the state eases over time or gets worse.
This line cannot be reliably drawn by the clock. The universal rule “never open the door while he is barking” can be simply harmful if the puppy is panicking, is in pain, or has an urgent physiological need.
On the other hand, not every sound means disaster either. What is needed is context, not an automatic reaction in either direction.

Why some puppies find it harder
Let us think about what has just happened from the puppy's side. He has lost familiar smells, warm bodies beside him and the whole rhythm of his day - in the space of a single day.
Now he is learning two things at once: that new people come back, and that a new place is safe. For a more sensitive puppy that is a great deal of work.
Australian Shepherds are often strongly oriented towards their people and notice changes in their surroundings very quickly. That does not mean they cannot learn to rest apart - they can, and they do. It only means that this ability should not be taken for granted on the very first night.
What we are really aiming for
The goal is not a puppy who stays silent in his crate at any cost.
The goal is a dog who is able to feel safe, to rest and to trust that his basic needs will be noticed. Then quiet comes of its own accord. It becomes a consequence of feeling well, rather than the only criterion by which we judge the night.
It is worth looking at the whole day, not only the evening. A puppy who is overtired, over-aroused or has had too little security will experience the night quite differently from one whose nervous system had chances to recover during the day. A night-time problem is often solved in the afternoon.

When extra help is needed
There are signs that are no longer a matter of stubbornness.
If, during confinement or separation, you see strong, recurring or increasing distress, attempts to escape, a risk of self-injury, heavy drooling, panic or a sudden change in behaviour - such a situation calls for an individual behavioural and, where appropriate, medical assessment.
The sooner ordinary difficulty settling in is told apart from a more serious problem, the less time fear has to take hold. Waiting rarely helps here.
Invitation: Our families are not left alone with the questions of those first nights. We will help you understand what your particular puppy is showing and when it is worth involving the right specialist.
Source: AVSAB Puppy Socialization Position Statement - crates and pens should be associated with safe rest and with play.