In this enum __Field structs for both variants generated like the variant contains flattened field, but that is true only for the second field:

#[derive(Deserialize)]
enum Enum<T> {
    Simple {
        a: i32,
    },
    Flatten {
        #[serde(flatten)]
        flatten: T,
    },
}

This is happens because has_flatten field in Container struct becomes true for enums if any variant contains #[serde(flatten)], but it makes little sense

For enums has_flatten should be bound to the variant, not to the enum