Lab reacted badly with Jack Russel puppy?

I have a five year old female black lab and my brother has a 4 month old Jack Russel. Now, since the puppy was not vaccinated and had a tough time adjusting (he was about 2 months old and raised outside -even in the cold-) we decided to only introduce short 3 minute sessions. Usually, my father or I held back erfly (lab) while someone held Sora (JRT) and let them sniff each other. Now, things were okay (he put his claws on her face and she did nothing. He licked her and my lab did nothing but sniff) but my father put Sora down and erfly growled and tried to bite him (I pulled her back quickly). Sora was slightly shaken, but then immediate went back to normal. erfly is now punished. However, how do I prevent this? I want them to get along and Sora is an inside dog while the other two are in the garage (I just want to be reured that if we have Sora out and if erfly gets loose she doesn't kill him).