The problem is that for the second case of airport (BBBB), the hash %in still takes into account the AAAA lines so the computation is made with the AAAA flights ....because you declared %in hash at the beginning and you are not reinitializing the same on your code (first foreach loop). You may change your code as

foreach my $airport ( keys %airport_hash){

    my @lines = @{$airport_hash{$airport}};
    my %in;
    ......
    .....
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