Welcome to the Forum.
I believe you are referring to the CloneDVD software program and not â€œCloneCDâ€.
I also believe you are referring to original Commercial DVD Movie Titles and not to â€œCDsâ€.
From the limited information you have provided it appears that you are selecting the â€œClone DVDâ€ option and not the â€œClone DVD Titles â€“ Clone a DVD including all titles and menusâ€ option. If you desire to make a BackUp copy that includes ALL the Season Episodes you need to use the â€œClone DVD Titlesâ€ option.
Suggest reviewing the below AnyDVD and CloneDVD User Guides ->