If your user(s) are logged in while the files are being backed up (which they are in this situation), then lots of files being used by various applications are indeed changing. (~/.local, ~/.cache and lots of other “dotfolders” in ~ are always being accessed and written to by applications that are running).
So, maybe try backing up specific folders that you know are not being written to: ~/Documents or whatever and see how that goes?
PS: I don’t know how backup tools are meant to handle this particular case, other than being like gnome-software and backing things up when these files are not in use. Maybe someone else will know.