The new growth that it is pushing is fresh juvenile/needle foliage - much stronger. I see this with junipers that have survived a period of stress and when they bounce back they throw a lot of immature foliage at the tips of mature/scale foliage. Just means the tree is on the right track. If I had to guess, the tree was either not fully recovered from being collected, or had recently been repotted and wasn't happy about it (?) I wouldn't do anything dramatic for a while - the tree needs some recovery time.
As Brian said, junipers will drop their old interior foliage. You just need to make sure it isn't due to fungus - particularly if you live in a humid area or have had tons of rain. We don't get rust here in Southern California, but we do get juniper tip blight (phomopsis). This last year we had a lot of rain and this spring was very hard on a number of my bonsai friends who got hammered by phomopsis. I have gotten very good at seeing what it looks like - and you don't have it - but if your juniper branches ever start to die from the tips inward - in spots here and there but not the whole tree - look up phomopsis and get ready to start an anti-fungal regimen.