You have carriage return whitespace at the end of your input, most likely because your input file is formatted with "Windows" newlines, that is \r\n.

Data::Dumper will show you that whitespace when you set $Data::Dumper::Useqq = 1.

Personally, I like to, instead of chomp, use s!\s+$!!, to remove all kinds of whitespace at the end of input lines.

If the file is known to have Windows line separators, I prefer to read it same way that windows does (use the :crlf IO-layer) and process it as a normal file rather than use a DIY solution.

use strict;
use warnings;
use Autodie;
use Data::Dumper;
my $file = \do{
    "Jay|Jay\@email|puppy|123 Street|Shirley\r\n"
   ."Travis|Travis\@email|puppy|456 Street|Emmy\r\n"
   ."Trisha|Trisha\@email|baby|789 Street|Eddie\r\n"
   ."Eddie|Eddie\@email|puppy|789 Street|Trisha\r\n"
   ."Shirley|Shirley\@email|baby|123 Street|Jay\r\n"
}; 
open my $fh, '<:crlf', $file ;
my @name_lines = <$fh>;
my %spouses;
my %people;
foreach my $line ( @name_lines ) {
        chomp($line) ;
        my @data = split '\|' , $line ;
        #map { $_ =~ s/[^a-zA-Z0-9_\@\. ]//g } @data ;
        #print Dumper \@data ;
        my ( $name , $email , $wishlist , $address , $spouse_name ) = 
+@data ;
        $people{$name}{email}    = $email ;
        $people{$name}{wishlist} = $wishlist ;
        $people{$name}{address}  = $address ;
        $people{$name}{spouse}   = $spouse_name ;
        #if ( $spouse_name ne '' ) {
        if ( defined $spouse_name and $spouse_name ne '' ) {
            $spouses{$name} = $spouse_name ;
        }
    }
    print Dumper \%spouses ;
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RESULT:

$VAR1 = {
          'Shirley' => 'Jay',
          'Jay' => 'Shirley',
          'Eddie' => 'Trisha',
          'Trisha' => 'Eddie',
          'Travis' => 'Emmy'
        };
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Bill

print Dumper \%spouses ;
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use Data::Dump::dd it has better defaults

print Dumper($scalar); # non-referential scalar
print Dumper(\@array); # scalar reference to @array
print Dumper(\%hash);  # scalar reference to %hash
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Devel::Peek is useful for inspecting data structures

you've obviously never used Devel::Peek to inspect data structures.