We have been seeing heterozygous X variants in male patients in exome sequencing studies. X heterozygosity (het variant in chr X / total variants in chr X) is up to 2% in male samples. There have been some question and answers about it on biostars too.

I looked into 1KGP to see where do these variants are coming from. My initial findings show gene families and pseudogenes. And I have suspicion and this situation is not specific to chromosome X.

You can see the details here:

https://omics.sbs/blog/XHetRel/1KGP_Xhet.html