This is interesting. We have a GSD and a chihuahua, they get along great! However, if I am on the floor with Pete (our shepherd) and giving him attention, if Paco comes by and pesters me for attention, Pete will pin him down with his paws until he goes away. I also notice this behavior if I have them outside at different times. As soon as Paco gets in the door, Pete will pin him again but only for a moment as if to say "know your role." They are so funny and it is so fascinating to witness the safe parts of their instinct that have survived domestication. Anyhow, I wouldn't worry about it unless there is a fear of harm being done.