Expected:
A bundle can hold 64 bee nests/hives regardless of there being bees inside.
Actual:
A bundle only holds a single bee nest/hive if there's 1 or more bees inside.
A bundle holds 64 bee nests/hives if they are empty.
Reasons why this behavior is a bug:
The change was not in the changelog, previously 21w19a and before? (Certainly in the snapshot that introduced bundles) It was possible to hold 64 bee hives/nests regardless of bee contents.
It also defies the rules that bundles follow: "Otherwise stackable blocks or items can be bundled up to their respective stack size", even bee hives with bees inside could theoretically be stacked (middle ctrl+click in creative to get a stack of NBT hives) Although unlikely, it is possible and therefore goes against this logic.
Other NBT items like filled maps are allowed stacked to their stack limit inside of bundles
It also affects the usefulness of a bundle.
Attachments include difference between bee nests in same version 21w20a and how treasure maps behave in bundles.
Probably intentional to prevent being used as an exploit to ban players.