Difficult to say without seeing them, as what you think is bullying might actually be playing. Can you describe the behaviour? How is it instigated? What is each dog doing? What noises (if any) are they making? What do they do at other times when the 'bullying' is not going on?

The one thing you will need to watch out for, even if they are playing is the smaller pup getting hurt, or beingtoo active, which might contribute to hip dysplacia in later life.