Usually it is fine for escripts and sometimes even desired for faster shutdown. The difference is that System.halt() does not shutdown the applications supervision trees one by one. It just halts the system.

I tried with…

defmodule Excript.CLI do
  def main(args \\ []) do
    {opts, _, _} = OptionParser.parse(args, switches: [halt: :boolean])
    if opts[:halt], do: System.halt(1), else: System.stop(1)
  end
end

…and could definitely reproduce the error, see:

$ ./excript --halt
$ echo $?
1
$ ./excript
$ echo $?
0

As @Phillipp says… it’s an issue with erlang escripts.