I am not sure about a beardie, but for snakes when they are scared of hands you have to work with them until they are used to it. A lot of time it is the animals personality but if you are concerned about the breeder you should ask to tour their facilities. You can look at the other animals and see if there are signs of abuse and reputable breeders will let you do this most of the time.
Ill take you through a typical process of working to tame a snake down.
Enclosure: The first thing you should do is move the enclosure to a less public place if it is in a high traffic area such as a living room. If this is not possible then you could put a few hides (beardies need a lot of space so this shouldnt be a huge problem) or put a background image on 2 or 3 sides of the cage (if 4 sides and a top are see-through.
Process: After getting the cage set up to be more private you can start to work with them. Ill say right now that for snakes it can take a week to many months depending, so if you truly want to get it comfortable with humans you should be prepared to put in a lot of effort. You need to be empathetic toward its fear as soon as you approach the enclosure. I am not sure what type of senses beardies have but snakes can smell (/taste) pretty decently. The first thing you need to do is get it used to your smell. You can do this by sitting next to the cage for a few minutes before opening or interacting with them at all. Also make sure to sanitize your hands after interacting with other pets because the smell of those pets could scare the beardie too. After doing this you should aim to pick the animal for short time period. I usually start with a 5-10 minute sessions per day until they seem comfortable enough with them. For you, that could look like the dragon not jumping, not fluffing, hissing, or bobbing their head. Once that is achieved you pretty much have what you want to teach them and can increase holding time and continue. When you increase the time you can just repeat the above. Just keep working with them until they seem fairly comfortable with you holding them.
I should mention that sometimes reptiles will never really grow out of their habits and if that is the case maybe consider keeping as a looking animal or rehome it as such?
Notes: Above is the basic process, but there are other things you can keep in mind. The first is when you first start holding him, make sure you do it over a bed or a couch. This will make falls or jumps a lot less damaging to him if they happen because the small body size can make those falls devastating. You can also kneel or sit and handle him lower to the ground. Another thing to consider is training the reptile to respond to certain triggers. for snakes this is feeding response training (if a snake thinks your hand is food and bites, you have to train them to not bite the hand). This is done with snakes by throwing a tiny bit of substrate on them when they feed so they know it is actual feeding time. The same can be applied to beardies too. If you train it to associate a tiny bit of substrate with getting picked up it may not be as scared because it knows what is coming. Another thing to remember is slow movements and try not to come from directly above. predators in the wild come from above so many reptiles are sensitive to this type of movement.
Hope this helps!