Leo skeletal anatomy! Click for better quality :)
The way most turtles actually fit into their shells is because their arms and legs are shaped to fit into the loose skin around the openings for their limbs, but on account of their human proportions, I just suspend my disbelief as to how mutant turtles could fit in their shells without the odd configuration to their organs that real turtles have. Real turtles have flat lungs that sit widely along their carapace, which is weird but cool. Turtles shed their scutes (the large flat scales on their shells and plastron) about once a year or if the scutes are damaged. The scutes have barely any skin between them and the bone, which is why turtle skeletons usually have the scutes on still, though they can pop off. The rest of the skin sheds regularly though, instead of in large patches.
For the brothers’, their respiration is much more human than turtle. Therefore, their lungs need to expand and contract with their diaphragm rather than just with their movement, so therefore they must have some flexibility to their chest. Some turtles, like box turtles, already have hinged plastrons, and softshell shells are mostly cartilage, so it’s not too far off to assume that there’s a bit of cartilage just to the upper plastral bones of the hard shelled brothers to give their humanoid lungs room to breathe.
Poor Leo. After the movie, one could assume he’s got a couple broken bones. It kind of made me morbidly curious as to how to describe injuries on a character whose skeletal structure is quite different from a human’s for my own writing!
Feel free to use as reference or disregard, these are just my own little speculations :)