You have to change your regular expression here

while ( <DATA> ) {
    my ( $key, $val ) = /^(\d+)\s+(\w+)/;
    $val = lc($val);
    $dict{ $val } = $key;
    }
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Try printing print Dumper \%dict and you can find the mistake

When I printed the $key and $value the result is as follows

my %dict;
while ( <DATA> ) {
    my ( $key, $val ) = /^(\d+)\s+(\w+)/;
    print "$key\t$val\n";
    $val = lc($val);
    $dict{ $val } = $key;
}
__END__
1       cross
2       reference
3       cross
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So the $dict{cross}=>1 is getting overwrite