Hey abwatson1,
Thanks for the question. If I understand correctly, iCloud Mail is marking things as junk that are not junk. I would recommend that you read these articles, they may be helpful in troubleshooting your issue.
iCloud: Identifying and filtering junk mail - Apple Support
Due to the complexity of accurately detecting and filtering out junk mail, on rare occasions a legitimate email from a friendly source may be blocked from reaching your Inbox. This is called a false positive.
If you feel that a legitimate email message was inadvertently filtered, you may want to ask your friend to send a follow-up email to verify that the issue exists. If you notice that multiple email messages are being delayed, bounced, or not delivered, contact iCloud Support. Also make sure to check your Junk folder for email messages that were incorrectly marked as junk mail. To check your Junk folder at iCloud.com, choose the Mail application and click the Junk folder in the sidebar. Email messages in the Junk folder are automatically deleted after 30 days.
iCloud: Manage junk mail
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Click the Junk folder in the sidebar.
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Select a message, then click the Not Junk button in the top right of the message window.
The message is moved to your Inbox. Subsequent email messages from the same sender are no longer automatically marked as junk.
Thanks for using Apple Support Communities.
Have a good one