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From SNPedia

Magnitude 5
Summary Data Quality Warning
Criteria Gs266/criteria

Some of your data claims that you have 2 Y chromosomes. In particular it is claiming heterozygosity for a Y chromosomal SNP.

While it is true that https://en.wikipedia.org/wiki/XYY_syndrome exists, the microarrays used by 23andMe, Ancestry.com and their analysis methods and others are prone to misinterpreting the sex chromosomes. As a result Promethease sometimes sees this in their raw data.

At various times, Ancestry.com has previously addressed this at http://ancestryforums.custhelp.com/posts/b7de792b84?commentId=30021

With a similar answer from 23andMe at https://www.23andme.com/you/community/thread/40845/

Even in those rare cases where you actually are XYY, it's likely that microarray testing would fail to detect it. This is because our understanding is that the two Y chromosomes in an XYY individual should be duplicates of each other, since they come about from a nondisjunction event in meiosis (II). As duplicates, they shouldn't show heterozygosity. In other words, even in an XYY individual, the Y chromosome SNPs should not show heterozygosity, which is why this genoset is a warning for poor data quality.

Additional discussion at reddit suggests the possibility of Pseudoautosomal region related issues