Cloning is what one does to make an exact duplicate of a partition or hard drive. It would help if you included your intentions here but I'd say it's correct that programs should be closed. This will be due to files that are in RAM which may have changed and need to be rewritten to the drive. Thus, changes will not be in the duplicated drive. Your example sounds like cloning software that installs to a drive and can be run from it. A better alternative that would not have that restriction is cloning software that's on bootable media. You boot to that media, select your source and target drives, and confirm your intention to clone the drive. This works well for drives that are of the same capacity but you might need to answer a few questions if they are not.
I see that most cloning software will ask you to close all running programs(Apps).
would this be best done in settings/privacy/backround apps? Or am I wrong with what the cloning software is asking. Example would say; Samsung Data Migration tool. Thanks in advance.