For CTAS queries, Impala has to do some gymnastics to figure out the path of the new table before the table has actually been created by the Hive Metastore. It looks like like that logic has a bug which prevents it from working with HDFS HA.
This issue manifests itself as follows.
When running a CTAS through the Impala shell you will see:
In the HDFS NN logs you may see something strange like this:
The problem is most likely in CreateTableAsSelectStmt.analyze()
Split the query into create table and insert into select.