Without a sample analyzed, I think the yellowing is likely due to excessive rain / wet soil causing low nutrients, overcowding of plants that interferes with air circulation and light reaching the whole plant, and mildew caused by the weather, the lack of air circulation due to plants be crowded, and the likelihood that the plants are one of the mildew-susceptible varieties (most garden phlox are). 

At this point, there is not much you can do as the leaves are already too far gone. They will likely drop off soon. Clean up all the leaves you can to reduce the mildew pathogen. Prune out any stems that are really bare and maybe not producing flowers. This will increase the air circulation. Fertilize the plants to replenish nutrients that may have leached through the soil as a result of the rain. In the spring, plan to dig, divide and replant your phlox, spacing them apart further to allow for light and air to reach the lower parts of the plants.