Aster yellows is caused by a phytoplasma (similar to bacteria) that is spread from plant to plant by leafhoppers. Symptoms usually start as yellowing of foliage. Plants may grow numerous thin stems, and flowers become distorted. From your description, it sounds unlikely that your marigolds were affected by aster yellows, although marigolds are susceptible to the disease. To prevent aster yellows, you can spray your marigolds with an insecticide to control the leafhoppers. Also, if you see signs of the disease developing, remove affected plants to prevent its spread.
The symptoms you describe sound more like those of phytophthora root rot. This widespread soilborne fungus causes lower leaves of African marigold (Tagetes erecta) to wilt and die. Stems may have a dark, water-soaked appearance. Death can result within a few weeks. The problem is worse in cool, wet soil. Phytophthora remains in the soil indefinitely, so it would be wise to plant something other than marigolds in this bed this year. Dwarf French marigolds (T. patula) are resistant to the disease. Other resistant or tolerant annual flowers are begonia, cockscomb (Celosia), ageratum, and geranium (Pelargonium).