When performing a full copy of a site, the permission inheritance of item/s is preserved in the target environment. However, it is not updated after performing an incremental copy.
Permission inheritance is not updated by Content Matrix on an incremental copy.
As a workaround, copy the site/list, then perform the Paste List Objects > Permissions action on the target after the incremental copy.

Note: Make sure to enable the Advanced Mode on the Settings tab of the Content Matrix Console to see all the other context menu options.