There are some errors. The one that blows up is:

my %stopwords = map { $_ => } <@excludes>;

If you print %stopwords in Data::Dumper you would have had:

$VAR1 = {
          '9999853' => '999986'
        };
[download]

And this is not what you want! In the map, you are failing to assign a value with each key. You could state that as:

my %stopwords = map { $_ => 1} @excludes;

Here I am assigning a value of '1'. It conveniently then tests true when you are looking for stopwords. I also removed the angle brackets around @excludes in your code, (that would be a glob, not what you want).

Altogether, it could be solved like this:

#!/usr/bin/perl
use strict;
use warnings;
use 5.012;
use Data::Dumper;

my $large =<<EOF;
9999853    5615    4    148656321
999986    5615    14    94873609
9999883    5615    4    860669
9999929    5615    4    73689618
9999931    5615    4    31286083
9999944    5615    4    148596445
999995    5615    10    78405504
9999963    5615    4    84291761
9999966    5615    4    5978256
9999979    5615    4    135953341
EOF

my $excludes =<<EOF;
9999853
999986
EOF


open my $fh1, "<", \$excludes or die $!;
my %stopwords = map {chomp; $_ => 1} <$fh1>;
close $fh1 or die $!;

open my $fh2, "<", \$large or die $!;
while( <$fh2> ){
        my ($test) = /^(\d+)/;
        
        # if $test is in the hash
        # then $stopwords{ $test } == 1 or true
        print unless $stopwords{ $test };
}
close $fh2 or die $!;

#print Dumper \%stopwords;
[download]