There is a bug in the cmb.js file for file_list file input which after all file or file_lists have been selected and then if user reselect some more files in file_list or file inputs then the result is appended in wrong file input.
I found the fix.
It was the wrong selector object used. Please correct it for others.
In cmb2.js inside cmb.mediaHandlers.list function change the selector for appending the result from :

    $formfield.siblings('.cmb2-media-status').slideDown().append(this);

to :

    jQuery('#'+cmb.formfield).siblings('.cmb2-media-status').slideDown().append(this);

at line number 232.
Hope that helps the plugin developer and community, wasted 2 days to fix this bug.