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.