Looking at the original code, a few things stand out:

• re-use of variable $file. Not wrong, but very confusing, certainly because you *do* use the (undeclared) @fruits filled in parse
• In the foreach loop, you use variables $name and $path that are never set (in that context)
• The first argument to split is a regex unless you want paragraph mode (and you don't)

Rewriting your program to show the data you got:

#!/usr/bin/perl

use 5.014002;
use warnings;

my @fruits;
my %info = parse ("test.txt");
# %info now holds:
# {   Albert           => {
#         apple            => {
#             path             => '/path/to/somewhere/a'
#             }
#         },
#     Dex              => {
#         jackfruit        => {
#             path             => '/path/to/somewhere/d'
#             }
#         },
#     Jack             => {
#         apple            => {
#             path             => '/path/to/somewhere/c'
#             },
#         pineapple        => {
#             path             => '/path/to/somewhere/b'
#             }
#         }
#     }

foreach my $name (sort keys %info) {
    foreach my $fruit (sort @fruits) {
        printf "%-7s %-12s %s\n",
            $name, $fruit, $info{$name}{$fruit}{path} // "-";
        }
    }

sub parse {
    my $file = shift;
    my %info;
    -e $file or return;
    open my $fh, "<", $file or die "Can't open $file: $!\n";
    say "-I-: Reading from config file: $file";
    my %seen;
    while (<$fh>) {
        m/^\s*(?:#|\s*$)/ and next;
        my @fields = split m/\s+/ => $_;
        my ($name, $fruit, $p) = @fields;
        $seen{$fruit}++ or push @fruits => $fruit;
        $info{$name}{$fruit}{path} = $p;
        }
    close $fh;
    return %info;
    } # parse
[download]

Will - with your test data - result in:

-I-: Reading from config file: test.txt
Albert  apple        /path/to/somewhere/a
Albert  jackfruit    -
Albert  pineapple    -
Dex     apple        -
Dex     jackfruit    /path/to/somewhere/d
Dex     pineapple    -
Jack    apple        /path/to/somewhere/c
Jack    jackfruit    -
Jack    pineapple    /path/to/somewhere/b
[download]