Creeping Lemon Thyme Developing Random Brown Sections

I have been enjoying the Creeping Lemon Thyme plugs that I purchased 3 years ago. They are filling in nicely. I have a question – what causes small sections to die out (turn brown)? The sections may be 8" x 8" and it can occur right in the middle of a vibrant green section of thyme – it is random, does not effect the health of the entire area, and eventually new growth from other sections fills it in – it is perplexing. Any thoughts as to why this happens?

It is not uncommon for low, creeping thymes to die out in seemingly random spots throughout a patch over winter. Thyme is fairly sensitive to microenvironmental factors that can vary over the area of a mat of thyme. Moisture, snow cover, drainage, freezing and thawing are all surprisingly varied over an area of the garden.
In addition, overcrowding in the spots where the original plants were planted can lead to rotting of the stems and roots while the younger parts continue to do well.
You don't indicate when the spots occur: starting in spring, thus implying that the spots are caused by death over winter, or during the growing season, thus implying that overcrowding and rotting could be the source of the problem. These are the main possibilities that spring to mind, but there are other, more remote possibilities also.
There could, for example, be a pest attacking similar to the patchy damage that grubs can cause in lawns. I have seen significant damage caused by ants as they dig around the entrances to their nests. A patch of Orange Spice thyme in my home garden, for example, suffered this problem and I had to plant something else in the spot where the ants seemed to have the upper hand.