Most likely the reason for this problem is the same as in your other post: you are using -outfmt 6 instead of pairwise alignment. Since blast is a local aligner, it will often find multiple high-scoring pair segments (HSPs) between two proteins, rather than a single global alignment. If there are 3 HSPs between a query and its match, that counts as a single hit and will be shown as a single line in pairwise alignment output (though it will be shown as 3 alignments in the alignment part of the output). Since -outfmt 6 doesn't show alignments, that single hit will actually be shown as 3 lines. Even though you are asking only for a top hit with -max_target_seqs 1, it will often show multiple lines because of HSPs. As I suggested to you before, try removing -outfmt 6 from your command-line just to see how that output looks like.