Use -- to separate the script's options from the options of the job, or even the job itself:

#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

use Getopt::Long;
GetOptions('file=s' => \ my $file,
           'dir=s'  => \ my $dir);

say "Running $ARGV[0] with the following arguments:";
say for @ARGV[1 .. $#ARGV];
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Example usage:

$ 1229381.pl --file file.1 --dir dir.2 -- some-job x y z
Running some-job with the following arguments:
x
y
z
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