Sure. There might be multiple titles on one DVD, which share the same video material. In theory you can put the same movie on one DVD many times, but change only small parts (ending, beginning, title sequence in different language, ....)
CloneDVD2 Quality bar is clever enough to detect "shared material".
In the example above, deselecting one movie will only change the quality bar a little, because only a small part (e.g., the alternate ending) was left out from the shared video material.