Years ago I grew tomatoes and peppers in the same garden, side by side. One of the tomato plants’ fruit seemed to acquire all of the properties of the bell pepper–hollow inside, with the seed cluster in the middle, towards the top–but it was still a tomato. I thought it was just a fluke, so I took the seeds and replanted the following year, with the same results. Do I have something here, or is this just one of several uncommon species that is already out there?
Although chiles and tomatoes are in the same family, Solanaceae, they cannot interbreed, and besides, this could not happen in the same year. For example, if you planted a serrano next to a bell pepper and they cross-pollinated, the hybrid would not appear until the seeds of either one were planted and grown out the following year. I think you have a coincidence here and you just had a tomato with a weird internal structure. That would explain why the tomato bred true to its original weird structure the second year–it was genetically embedded in the tomato. There are very strange-looking tomatoes out there, including black tomatoes, tomatoes with fruits only 1/2 inch in diameter, and tomatoes that stay green. The closest to what you describe is a variety called ’Striped Cavern’, which looks very much like a bell pepper on the inside.