Are you sure your arrays contain what you think they do? See Basic debugging checklist. Since you haven't provided your literal input files wrapped in <code> tags (see How do I post a question effectively?), it's hard to be helpful. Two possibilities I see:

1. Your second open is failing, and thus you don't know that @array1 is empty. It's probably better if your opens look more like: open(FILE,'<', $file) or die "Open fail on $file: $!"

2. Your input is literally 1,2,3,4 and so your arrays only have 1 element. In this case, you need to reformat your input files to be newline separated or feed the input through split.

The following code works for me.

#!/usr/bin/perl -w
use strict;

use Array::Utils qw(:all);

my @first = (1,2,3,4);
my @second = (1,5,6,7);
my @minus = array_minus( @first,@second );
for my $term (@minus) {
    print "'$term'\n";
}
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It outputs

'2'
'3'
'4'
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