if ($_ =~ $identifier{$pins1.}) {
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This doesn't work. {$pins1.} is a syntax error. There is no wildcard lookup in a hash.

    $vline =~ s/^\S+//; #trim leading space
[download]

Nope. \S is non-blank.

my (undef,$scenario, $pins1, $threshold1, $newthreshold1, $diff, $stat
+us) = split /\s+/, $wline;
[download]

Your key is ending up in $scenario here. Skip the undef.

If you encounter an identifier with a wildcard in the waiver file, you need to rewrite that identifier as a valid perl regular expression and later match each key of the waiver hash against the current $pins1:

#! /tools/perl/5.8.8/linux/bin/perl

use strict;
use warnings;
use Data::Dumper;

# Source script
my $report = $ARGV[1] ;
my $waiver = $ARGV[3] ;
my $result = $ARGV[5] ;

# Set up a hash to receive the information
my %identifier = ();

# Read the violations file into the hash
open my $filter, '<', $waiver or die;
while (my $vline = <$filter>) {
    next unless $vline =~ /\S/; #skip blank lines
    print $vline;
    $vline =~ s/^\s+//; #trim leading space
    my ($pins2, $threshold2, $newthreshold2) = split /,/, $vline;
    $pins2 =~ s/\*$/.*/; # make key into regex string if trailing *
    $identifier{$pins2}{'threshold2'} = $threshold2;
    $identifier{$pins2}{'newthreshold2'} = $newthreshold2;
}
close $filter;

print Dumper \%identifier;

# Read input file line by line and compare 2 files
open my $input, '<', $report or die;
open my $output, ">", $result or die;
while (my $wline = <$input>){
    my ($scenario, $pins1, $threshold1, $newthreshold1, $diff, $status
+) = split /\s+/, $wline;
       # overwrite values if match
    for my $key(keys %identifier) {
        if ($pins1 =~ /^$key$/) {
            if ( ($threshold1 == $identifier{$key}{'threshold2'}) && (
+$newthreshold1 <= $identifier{$key}{'newthreshold2'}) ) {
                $status = '(WAIVED)';
            }
            last; # skip remaining keys of for()-loop
        }
    }
    printf $output "%-44s   %-24s   %-8s        %-8s        %-8s  %-10
+s\n", $scenario,    $pins1,     $threshold1,         $newthreshold1, 
+       $diff,  $status;
}

close $input;
close $output;
[download]

Close your filehandles as soon as you are done with them.