That’s called a replay attack and is absolutely something e2e encryption protects against

There are actually three different things: replays, reloading a message, and delayed messages. Replays are impossible in the signal protocol, so that’s not what happened. Delayed messages is part of signal: you can receive message2 before message1. Reloaded message is probably what happened, it doesnt work at the signal level since “deleting a message” is not something signal specifies.

e2e encryption means the party in the middle does not have the key to the data. It is somewhat of a misnomer since it is a feature of key-agreement more than a feature of encryption.

Any other features are dependent on the protocol that uses the secret key. You will generally see an encryption method that is protected against cipher-text manipulation, but e2e does not guarantee that. Similarly, a protocol that uses e2e encryption can add replay protections, but it is not at all a feature inherent in e2e.

I could well imagine that whatsapp has some replay protection build in. I could similarly imagine they have a way to override that in case they need to. Heck, perhaps the replay protection is implemented with WhatsApp as the ultimate arbiter of what counts as a replay. As long as WhatsApp does not know the key used to encrypt my messages, the encryption is e2e in my book.