I noted in bug ticket #205 that this issue was fixed for release 2.0.7; but it seems to be present in release 2.1.0.
I use --un flag to capture unaligned reads to a fastq file for a subsequent alignment step. When I add --no-unal to drop those same unaligned reads from the SAM output, then they also don't get written to the unaligned fastq file (the file gets created, but no records get written).
Command line that causes the bug:
bowtie2 -q --phred33-quals --very-sensitive -k 10 --un PL02.not.genomic.fastq --no-unal --threads 4 -x Pf.genomic_idx -U PL02.not.ribo.fastq 2> PL02.Bowtie2.AlignMetrics.txt | samtools view -bS -o PL02.genomic.bam -