https://github.com/samtools/samtools/issues/359
rmdup with no option (neither -s nor -S) expects alignment pairs with alternating +/- TLEN values. It is a special-purpose tool for removing PCR duplicates which conform to that pattern.
The warning is issued for consecutive positive TLEN values. A simple contrived example:
cat rmdupExample.sam
@SQ SN:c2 LN:9
s1 67 c2 1 0 9M = 1 30 CTAATAATC XXXXXXXXX RG:Z:1st
s1 67 c2 1 0 9M = 1 -30 CTAATAATC XXXXXXXXX RG:Z:1st
s1 259 c2 1 0 9M = 1 30 CTAATAATC YXXXXXXXX RG:Z:2nd
s1 131 c2 1 0 9M = 1 30 CTAATAATC XXXXXXXXX RG:Z:3rd
s1 131 c2 1 0 9M = 1 -30 CTAATAATC XXXXXXXXX RG:Z:3rd
./samtools view -b -o /tmp/rmdupExample.bam /tmp/rmdupExample.sam
../samtools-0.1.19/samtools rmdup /tmp/rmdupExample.bam /tmp/test_input_1_rmdup.bam
[bam_rmdup_core] processing reference c2...
[bam_rmdup_core] inconsistent BAM file for pair 's1'. Continue anyway.
[bam_rmdup_core] 2 / 3 = 0.6667 in library ' '
./samtools view /tmp/test_input_1_rmdup.bam
s1 67 c2 1 0 9M = 1 -30 CTAATAATC XXXXXXXXX RG:Z:1st
s1 259 c2 1 0 9M = 1 30 CTAATAATC YXXXXXXXX RG:Z:2nd 