One possibility is that they are resting on the ground, this can bruise the tomato and cause browning. The other is that you have pests on your tomatoes.
The brown spots on the bottom of your tomatoes are called Blossom End Rot. Some say it's because they received too much water too fast. Others say it's a fungus. Either way you should pick them and throw them away. Do not compost. Your plant will make more tomatoes. Enjoy!