Unfortunately you don't say where you live so I can't say if it's the climate.* These shrubs don't do well outside of arid climates.* Here's some info on a couple of fungal problems these shrubs can have. Take a look to see what might fit what you are seeing.* Your juniper would be Juniperus scopulorum 'Wichita Blue'.* Your particular variety isn't listed for resistance of these fungal problems.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.