Those brown needles down at the base of the shoots looks normal to me. Even though juniper is evergreen, individual leaves are only good for a couple of years. When they start to get old the tree switches them off and they die. In the meantime new leaves have grown from the tips of the shoots so the tree always has fresh, active leaves.
You can see that this means continuous growing for evergreen trees. Eventually you will have long, bare branches - not very attractive for bonsai. Growing evergreen bonsai is a continual process of growing then cutting back to maintain the desired shape. Long outer shoots are removed and inner ones replace them to keep the compact shape.
I'm sure someone will post a reference to a better explanation or tute with pics.