Agreed, "Limitations" is the right place for this.
"Version" has a different purpose (explaining that native support for Parquet was added in Hive 0.13.0) so its title should probably be changed to reflect that information. "HiveQL Syntax" discusses a syntax change with native support, so it could become a "Version" subsection.
"Limitations" might need a new title too if it turns into a list of changes, or a new section could be added for that. But for now I think we can just put this issue in "Limitations" without changing any headings.