There are two options
Enable auto selection of removed streams: (shouldn't that be de-selection Olli?)
This selects a different steam as default from the one normally played when you insert the DVD in the player, in other words instead of automatically playing what the DVD was originally written to play (for example English audio with Mexican subtitles) you may have removed the English audio stream replacing it with the Italian audio stream and selected German for the default subtitles.
Filter unreferred material to improve splitting:
Supposing you split a DVD into two separate DVDs because it is too large to compress and keep the quality you desire, when you split the original DVD into two separate selections there may be material that is no longer necessary as it cannot be accessed from one half of the DVD so CloneDVD will try to remove this.