I don't know the exact motivation but as it seems, this problem occurs when OS X Server is installed in the source system (see Apple Support Community discussion). There, the recommendation is to uninstall OS X Server before the migration. However, this obviously does not work in all cases.
As a better alternative, use the tmutil restore
command for the files/folder to be restored. For example to restore the home of user "foo"
tmutil restore /path/to/Backups.backupdb/computername/Latest/diskname/Users/foo /Users/foo
Before that, create the user and ensure it has the same user-id as in the old system.