jstest to reproduce the issue is attached.

Imagine we create an index with partial filter expression {location: $geoWithin: <polygonA>}.
And query the collection with filter {location: $getWithin: <polygonB>}.

During planning, isSubsetOf(index filter expression, query expression) will be called to determine if index can be used.

It will check if polygonB is inside polygonA: https://github.com/mongodb/mongo/blob/04299d14a33a89023b6bc69d8d59a618aa603e5d/src/mongo/db/matcher/expression_algo.cpp#L750

GeoMatchExpression::matchesGeoContainer has an explicit check to never match big polygon, which fails for some reason
https://github.com/mongodb/mongo/blob/04299d14a33a89023b6bc69d8d59a618aa603e5d/src/mongo/db/matcher/expression_geo.cpp#L415

And GeometryContainer::contains is called that fails if the other container is a big polygon:
https://github.com/mongodb/mongo/blob/04299d14a33a89023b6bc69d8d59a618aa603e5d/src/mongo/db/geo/geometry_container.cpp#L322

It looks like the bug can be triggered easier by just inserting a document with big polygon and querying if it is within another geometry, but for some reason, the only way this actually breaks in partial index filter.