This can be reproduced by this test https://github.com/elastic/elasticsearch/blob/main/server/src/test/java/org/elasticsearch/index/mapper/blockloader/GeoPointFieldBlockLoaderTests.java#L77. geo_point fields have custom handling of arrays and therefore synthetic_source_keep: "arrays" should not apply to it (arrays have special meaning so we don't know how to exactly preserve them). However we put values of geo_point field in _ignored_source in some cases.