BWA properly paired reads are not really properly paired?

[metheuse]

I selected properly paired (and mapq>=4) reads from BWA alignment by running:

samtools view -h -f 2 -q 4 -b

Flagstat shows that this did remove most of the reads that have mates on different chr. However, several remain:

5 + 0 with mate mapped to a different chr
4 + 0 with mate mapped to a different chr (mapQ>=5)

Why is this?
Thanks.