Various problems can cause sex determination to be inconclusive (intermediate read dosage):
check library-level bams, to exclude bioinfo issues with accidentally merging libraries from distinct individuals
filter reads with low MAPQ (e.g. < 30)
ensure mito reads are excluded - some samples can have high MT/nuc ratio and if there is no mito sequence in the reference, the mito reads can map to NUMTs instead
Various problems can cause sex determination to be inconclusive (intermediate read dosage):