What's up with my tomatoes?
Based on your photos there are several factors that you have to consider. The tomatoes with black bottoms looks like blossom end rot, a common nutritional disorder. Symptoms are most often seen in paste type or plum tomatoes. This looks like the type of tomato you are growing. Remove the tomatoes that are affected and discard. Regular, deep watering will alleviate the problem if calcium levels in the soil are adequate. See more on blossom end rot http://extension.umd.edu/growit/blossom-end-rot-vegetables
The tomatos in the containers look leggy and thin and looks like it is stretching for the light. Plants receiving insufficient sunlight become weak and spindly and produce fewer blossoms and fruit. You did not mention how much sun the plant receives. They require a minimum of 6 hours of direct sunlight and will be more productive in 8-10 hours of sun.
Also, the containers do not look large enough for the plants and you have two tomatoes in one container. They are competing for moisture and nutrients. A regular size tomato requires a 5 gallon container. A patio type tomato may be planted in a smaller container. Tomatoes in containers may require daily watering during hot summer months and good drainage and may need to be fertilized lightly every two weeks for a continuous harvest.
Here are some links that you may find helpful.