It could be Phomopsis (fungus) or one of it's cousins or it could be Juniper twig girdler (insect) or it could be pet urine. Drought and mechanical damage is another possibility.
I don't think it has to do with pruning with shears because some of it is on foliage that doesn't have any pruning near it. I looked up the fungus and I don't think its that because its in small amounts and spread all over the tree, but I really don't know for sure. I couldn't find any signs of a girdler, but I did find a spider living in the apex of the tree. Could that be it? Thanks for the suggestions.