Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?
There are homologous regions between X an Y chromosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region

It is therefore normal to have some female-derived reads mapping in Y chromosome.

You should probably check what proportion of such reads fall in other parts of the Y chromosome than pseudoautosomal regions.