Others have determined the problem. My suggestion is to use a more perlish style. I offer:

#Searching for NCBI Entrez Gene IDs
my @OriginalArray = ( $Text =~ /(LOC\d{9})/g );

for my $loc( @OriginalArray){
        next if $VisitedLinks{$loc};

    $VisitedLinks{$loc} = 1;
    my $Link = $self->EntrezGeneLinks($loc);
    $Text =~ s/\Q$loc\E/$Link/g;
}
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