Hi Todd, I believe this is intended behaviour.
If you open a file without checking it out and then save, you are creating a new file effectively.
To keep your modified changes and create a new version of the same file, you will need to check out, make changes, save locally, then Check in.
However, if you modify a Part in and Assembly, exit Part without saving, and Assembly is NOT checked out, it will let you Check Out the Assembly and create a new Version of the Assembly? this makes no sense.... I have submitted this to our VAR, hoping this gets flagged as a bug.
If I understood well in 2012 you can save modified files even it is not checkout. In my opinion this is an abnormal behavior because a file that is not checkout is like read only file so you can't save it.