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I've noticed the same situation in some threads on my own instance too. But I'm under the impression that it might just be backlogged on the responsible instance that's supposed to send out the federated content. I've noticed this when just having my home feed set to New and then suddenly seeing like thirty posts from lemmy.world come across all at once with widely varied timestamps.
I suppose the best way to test if this is the case would be to note down any threads that are missing substantial amounts of comments on your local server and then check back with that thread periodically to see if and when they start to fill in.