Are you sure you're actually getting the result you think you're getting? Specifically, it really sounds like the line number should correspond to your print "$item"; line. And "Use of uninitialized value in string at..." is a warning, not an error (unless you're doing something strange). I'd suggest that you look at what exactly is in your hoa before the loop. Here's test code that works just fine.

#!/usr/bin/perl
use strict;
use warnings;

use Data::Dumper;

my %hoa = (
    a => ["apple", "aardvark"],
    b => ["banana", "bandana"],
);
        
foreach my $head (keys %hoa) {
    my @data = @{$hoa{$head}};
    my $item = shift(@data);
    print "$item,";
}

print $/;
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which produces as output

apple,banana,
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