My first thought is blossom end rot, a common tomato disease. And no, it's not how they're supposed to grow, but it happens a lot. Uniform watering (mulching helps keep the soil evenly moist between waterings) is a good start... I found once I mulched my tomatoes I rarely had problems with blossom end rot. I've included a link below with more information (scroll down), and if you google it you'll find lots more, and others here will probably have other suggestions. Good luck!

Here is a link that might be useful: blossom end rot

Brown on bottom of green tomatoes....newby needs help please!!!!

My Charity tomato plant has lots of green babies..but the larger ones, are flat on

the bottom and brown....I am reading about blossom end rot.......what can I do to save these...I am first time growing tomatoes....these are in a very large pot...I use tomato tone fert...as suggested on container...and thought I was watering sufficiently...but need your help.

The problem that causes blossom end rot happened early in the tomato's development, often weeks before the rot becomes visible to the gardener. You can't really do anything to save those tomatoes. If the BER is minor (just a small spot) and the "dry" type (not wet and mushy), you can let those tomatoes continue to grow and ripen and just cut off the dark part when you eat them. If the BER covers a lot of the bottom or is the mushy, wet type, you should cull and discard the tomato so the plant can put more energy into the fruit that is not affected.

Watering needs to be consistent in containers. Both conditions that are too wet and too dry can trigger BER, as can letting the plant swing back and forth between conditions that are too soggy and too dry. It's a tricky balance and can depend on what kind of medium you're growing in, how much moisture it retains, etc. A really well-draining medium that you water deeply and frequently seems to works best. If you don't have a well-draining medium, you have to stick your finger down in the mix and feel for moisture levels. If very wet, don't water yet. In the hottest part of the summer, you should probably check moisture levels twice a day.

A lot of people report better results with liquid fertilizer in containers. The granular organic ferts rely on soil microbes and composters to break down nutrients and make them available to the plants, and containers just don't have as robust of an ecosystem.

If you are growing in containers and not fertilizing frequently or just using fish emulsion or something, BER could be caused by calcium deficiency. Soil calcium deficiency is less likely growing in the ground, and watering is more likely the culprit there.

There is a container gardening forum where you can get a lot of information about the challenges of container growing.