Conquer Blossom End Rot. If you see a dark, rotting spot on the bottom of your tomatoes, it’s blossom-end rot. This problem, caused by a calcium deficiency, can be solved a few ways. When tomatoes, peppers, melons, and eggplant develop a sunken, rotten spot on the end of the fruit, the cause came long before you found the problem. It’s called blossom end rot, and here is why it happens.