It appears that lines with  -// are included because you don't anchor the pattern  /\s+\/\// to the beginning of the line. So it looks like you probably want something like:

open FH, '<', $file or die "could not open '$file' $!";

my @arr;
while ( <FH> ) {
    chomp;
    push @arr, $_ if s!^\s+(?=//)!! ;
    }

foreach ( @arr ){
    print "$_\n";
    }
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