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The problem with hive indexing when dealing with partitioned tables is that the index is created on the entire table instead of just one partition, which can be inefficient and slow down queries. This is because hive indexes need to be rebuilt every time a new partition is added or an existing partition is modified. Additionally, the size of the index becomes too large to handle efficiently as the number of partitions increases. To overcome this problem, it is recommended to create partition-specific indexes or use an external indexing system like Apache Solr or Elasticsearch.