I see. Is there any way to stop this from happening? With this problem in mind, I'm not sure how to design a ship that travels far and does not stay in one big piece. Out of curiosity, if this is the case, how do other people go about making landers for ships on long-duration missions?
Edit: I think I figured it out! DStaal, you were right, it seems to totally be about the staging. From what I've tested, it seems to be dependent on what the root of the spacecraft is. If the root of the craft had not been on the return capsule when I had staged, it would have counted as another spacecraft when it jettisoned and everything would have worked as expected.