I think the problem lies in the 2 loops you have set up Pedro.

foreach my $position1 (@{$file1{$key}}){

This array holds the position +/- 8 that you read from the first file. Then, further down in your code, you are also adding plus/minus 8 postions from the position you read from the second file.

foreach my $pos (@range){

So I believe that is why you are getting the redundant printout.

Chris