This can happen if you uploaded a lot of messages using a desktop mail app, maybe when migrating to a new mail provider, or moved a lot of messages to a new folder.

Can also be caused by a server issue, since IMAP guarantees ordering by date for incoming mail.

To troubleshoot these and other similar scenarios, simply change the "Messages to sync" setting in Settings > Manage accounts > Your account > Options > Account Options from "by message count" to "by time period".

For migrated accounts, if you’ve uploaded your messages some IMAP mail servers will then assign the date and time of upload to all messages. If you’re seeing this, please: Delete the account in Aqua Mail and add it again > Before it synchronizes messages open the account’s Options and folders > IMAP options > Change “which message date/time to download” to “Date/time sent (from message header)”.