I strongly recommend using strictures (use strict; use warnings;), although that is not what is biting you here. In fact your code performs as I would expect (although normalizing whitespace in names would be a good idea - 2 entries for Bob Wilson):

use strict;
use warnings;

my %bigList;

while (<DATA>) {
    chomp $_;
    next unless length;
    
    my $inp = $_;
    my $client = $inp;
    my $num = $inp;

    $client =~ tr/0-9().-//d;
    $num =~ tr/ a-zA-Z().-//d;
    
    #make big list
    $bigList{$client}{$num}++;
}

for my $one (sort keys %bigList) {
    print "$one ", join ', ', sort {$a <=> $b} keys %{$bigList{$one}};
    print "\n";
}

__DATA__
Wanda Smith (332)432-9887
Freddie Sonere 442-9089
Bob Wilson 332-454-9932

Bob Cartwright (821)987-0089
Felix Harris 433.344.8711
Bob Wilson (888)821- 2248

Sam Burr 455-0327
Gloria Simpson (821)544-9341
Wanda Smith 444-9721
[download]

Prints:

Bob Cartwright  8219870089
Bob Wilson  3324549932
Bob Wilson   8888212248
Felix Harris  4333448711
Freddie Sonere  4429089
Gloria Simpson  8215449341
Sam Burr  4550327
Wanda Smith  4449721, 3324329887
[download]