We were unfortunately missing test coverage for this relatively basic scenario (non-nested collections are covered and work fine).
The following fails:
[ConditionalFact]
public virtual Task Index_on_nested_collection()
=> AssertOrderedCollectionQuery(() => AssertQuery(
ss => ss.Set<RootEntity>().Where(e => e.RequiredAssociate.NestedCollection[0].Int == 8),
ss => ss.Set<RootEntity>().Where(
e => e.RequiredAssociate.NestedCollection.Count > 0
&& e.RequiredAssociate.NestedCollection[0].Int == 8)));