Sex inconsistencies in Plink - Affymetrix array

Question

[Mari]

I have recently run the following steps in Plink(1.9) to check the sex against the recorded sex of participants. However I am still getting 65 errors. All of them are recorded as female, but coming up, very clearly as male, using the F-statistic. See plot below.

I have tried several iterations of the process but with not luck.

I am however, getting a lot of hetero haploid issues (which I removed using set-hh-missing), and this did reduce the number of mismatches however did not eliminate them. I also get a Warning: non-missing y chromosome detected

Could it be anything to do with that? Any thoughts or input is appreciated. This was using an affymetrix array I have also double checked all the sample recoding and there's no issues there

Steps:
--chr 23-24 --maf 0.01 --geno 0.05 --mind 0.05 --hwe 0.000001 #QC variants
--exclude rm_dups_atcg
--split-x b37 
--indep-pairphase 20000 2000 0.5 #extract prune.in
--set-hh-missing
--check-sex ycount #0.2 and 0.8 are my sex thresholds, which fits the data