The thistle growing amongst your juniper bushes may be robbing them of nutrients and water. It's best to control thistle as soon as you notice it. The longer a stand exists, the deeper its roots go. The best way to get rid of most types of thistle, while protecting your juniper bushes, is to physically remove it. But thistle is a tough plant to kill. It will take several years of consistent culling to finally starve the thistle's roots to death.
Cut musk and other biennial or annual thistle down to ground level before the thistle buds begin to develop their color---these types of thistle only reproduce by seed. Cut Canadian thistle as soon as you spot it. Remove all of the weed's plant tissue from the area; thistle seeds can still mature even after the thistle's head has been cut.
Dig up any Canadian thistle plants whose roots do not interfere with your juniper bush's roots. Use a trowel and be sure to remove all the roots---even small thistle roots can regenerate to grow new plants.
Cut or mow any Canadian thistle plants that regrow before they reach 3 inches in height. Continue cutting---it may take several years---until the thistle's root system is too starved to produce new plants. Cut other annual or biennial thistle plants before their flowers develop their color.