I have never had that problem, but I've heard that certain heirloom varieties will just do that naturally. There is a "fasciated fruit gene" that does it. Also, it's well understood that potassium deficiency can result in tomatoes that don't completely ripen. That is, the outside might look nice and red, but the inside may remain hard and green. Of course, potassium deficiency will show up in foliage abnormalities as well.

Most of the research i have read on the issue seems to tie it to one of the stress factors. Insufficient potassium as Dan mentioned or a maldistribution of K due to inconsistent soil moisture levels during ripening is one. Other stress factors can also play a role - exposure to temperature extremes, drought, excess fertilizer, etc. And variety too plays a role in that it is apparently less of an issue in newer hybrids than in the open-pollinated varieties.

Dave