It means the gene has multiple copies in the pseudoautosomal regions. The '.1' part is the version number.
How you deal with them most likely depends on whether you care about these regions.
Just found out that these suffixes are added in the GENCODE annotation files. We need to discuss how we deal with these because we can't be putting out IDs with one hand and not providing tools that can interpret them with the other hand.
I'm sorry for any confusion.