Have heard that keeping them together will sometimes stunt the growth of the little one, also the big one has slowed down recently, and from what I have seen from bearded dragons he is not full size yet, hes about 6-7 months and the other was a little smaller to begin with so shes probably 4-5 months old, anyways they have been caged together since, until recent when they were seperated because I read that it is bad for them when they are together cause they are dominating, though when I put them together occasionally they do show dominance/submission, the big one will bob his head and the girl will wave her arm, the big one doesnt get dark or anything though and sometimes he will puff up. Is this accurate that this is why the girl is so small still?
I had the same issue with Reptar and Chomper. I took them to the vet for a check up and he said that it may be because Chomper is so dominate, he probably tries to steal most of the food and the best basking spots. After I separated them, Reptar started putting some weight on. I would keep them separated so you don't have any other issues.