while (<$fh>) {
   my ($key, $pos) = split /\s+/;
   $positions{$key} = $pos;
}

Needs to be replaced with:
while (<$fh>) {
   chomp; #line added
   my ($key, $pos) = split /\s+/;
   if (!$positions{$key}) {
     $positions{$key} = $pos;
   } else {
     my $ref = $positions{$key};
     push @$ref,$pos;
   }
}
and also replace: for my $key ( sort keys %positions ) {
   .......
}

with:

for my $key ( sort keys %positions ) {
   my $ref = $positions{$key};
   foreach my $value (@$ref) {
     .......
   }
}
As the key can hold multiple values the hash contains an array

In reply to Re: Multiple Key Problem help by u671296
in thread Multiple Key Problem help by ashnator

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