After successful hard drive cloning some files that appear in the result of existing files not deleted files are with wrong data and of course they can't be viewed,it means when I open these files with hex editor they with real name but with unknown data and without header inside.
Can someone explain this phenomenon?
Is it because of wrong information in MFT(although the reading of the sectors in this area was successful)?

Either file system points to wrong clusters or it points to correct clusters but they were overwritten. Since you tell us nothing about how data was lost and what was done/used to recover files that's about as specific as it gets.

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Joep - http://www.disktuna.com - video & photo repair & recovery service

It happened on several drives with bad sectors but with 100% of drive imaging success.
Also in direct file explorer access with mrt and also by recovering the image file in third-party software.
A very small amount of files with this phenomenon.
These files cannot be repaired using software.

It could files inside folders (lost folder or whatever the software you're using calls them) that are not connected to file system for some reason and don't have status 'deleted'. Screenshot might help. Sometimes file access, modification dates can help, like if they're older than creation date of current MFT it may be remnants of a previous file system.

_________________
Joep - http://www.disktuna.com - video & photo repair & recovery service