You don't say which variety of prostrate juniper you have and you might not know, but the 'Blue Chip' is a common one and tends to dry out and get brown in the center as it gets older. Here's a quote from this site.
It may just be time to replace them if you can't discover any other problems mentioned in the article.
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.