Several Problems:

  while  ($line = <$fh>) {
  chomp (@r = split/\s+/);
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You read into $line, but you are split()'ing $_ (and you'll probably want to use the special case split: split " ", $line.

     push @{$lineFileContains{$r[3]}}, [@r[4..$#r]];
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Your indices seem a little too high to be grabbing the last two elements from a 5 element list (ie, [4] is the last index)

               foreach (@{$lineFileContains{$_}}) {
                 print "\t$_->[3]\t$_->[4]\n";
               }
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If the array you pushed onto your hash was only supposed to have two elements, why are you trying to access the 4th and 5th elements in the array?