That's a very unsafe way of doing things! You should be calling encrypt once, not once per line.
encrypt(join("\n", @$input), $key)
I do get garbage at character 32 (or thereabouts, I didn't look closely) when I use your version. I didn't spend any time finding out why because it goes away if you encode once as I urged you to do above.
...
my ($action, $file, $key) = @ARGV;
my $input;
{
open(my $fh, '<', $file)
or die("Can't open $file: $!\n");
binmode($fh);
local $/;
$input = <$fh>;
}
if ($action eq '-e') {
print encrypt($input, $key);
} else {
print decrypt($input, $key);
}
$ diff -au a.pl <( perl a.pl -d <( perl a.pl -e a.pl key ) key )
$
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