I'm guessing it's a migrated account (emails copied from somewhere else, or maybe your ISP used to self-host and just now moved to Yahoo)...
... and no it's not unique to Aqua, happens in other mobile mail apps too (which just like Aqua don't download the entire mailbox).
Please see the FAQ under: Messages out of order, or wrong message dates
In short:
- Please long press on the account (on the app's main screen) -> options and folders -> account options
- change the “Messages to sync” setting from a number based value (like “25” or “50”) to a date range based value (like “7 days” or “14 days”).
- back out and refresh the account / folder