Search API did not find any entities of type 'ENTITY_TYPE'.

When cron runs to index items, I get a lot of the following message: Search API did not find any entities of type 'node'.

The search_api_denormalized_entity table contains index_ids that are not in the search_api_index table, and many rows for these non-existent indexes have needs_processing set to 1.

So there must be something wrong with how the indexes are managed, maybe? I don't think non-existent indexes should be referenced.