Is there any reason that I would get duplicate rows after a join using the Python TableAPI? Have verified that all values which I join on are unique in each of the two input tables to the join.

Have you looked at https://nightlies.apache.org/flink/flink-docs-release-1.17/docs/dev/table/concepts/dynamic_tables/? Flink can emit multiple rows with the same PK whenever there is a match in either of the join sides.