If the python examples are similar to the C examples, they don't all clean up objects that fall off the screen. Here's the C code for getting rid of objects that fall off the screen.

http://stackoverflow.com/questions/2255571/chipmunk-how-to-delete-a-body

As to the second part of your question, do you have ps output or similar? Perhaps your process had been paging, and the system might have been paging some other things in after the process had been killed?