If I have the input files
file1.txt:

1.he is man
2.don't you
3.xyzzy
4.what goes on
[download]

and
file2.txt:

he is
z
what are
try to do
[download]

and I run the script
pm_11118096_1.pl:

# pm_11118096_1.pl                                          15jun20waw

use strict;
use warnings;

my $file1 = 'file1.txt';
my $file2 = 'file2.txt';

open my  $h2, '<', $file2 or die "cannot open file2";

my @a2 = <$h2>;
close $h2;
chomp @a2;
my $match = join '|', @a2;
$match = qr/$match/;

open my $f3,'>',"do.txt" or die "$!";
open my $h1, '<', $file1 or die "cannot open file1";
my @a1 = <$h1>;
close $h1;

print grep {$_ !~ $match} @a1;
# print $f3 grep {$_ !~ $match} @a1;
[download]

I get the following output:

c:\@Work\Perl\monks\Sidd@786>perl pm_11118096_1.pl
2.don't you
4.what goes on
[download]

If I comment out the
    # print grep {$_ !~ $match} @a1;
line and uncomment the
    print $f3 grep {$_ !~ $match} @a1;
line, I get an output file do.txt with the content

2.don't you
4.what goes on
[download]

(and no output in the command window).

When you run your code with these input files, what do you get?