How many users in your organization encountered the issue regular messages moved to junk folder? Did you configure any 3rd party spam filter for your organization?
In Exchange side, we could check if there is any related information recorded in the message trace log why the mails are moved to junk folder.
Also, we could disable the junk email rule on all users with below command, introduced in the official document: Configure junk email settings on Exchange Online mailboxes
$All = Get-Mailbox -RecipientTypeDetails UserMailbox -ResultSize Unlimited; $All | foreach {Set-MailboxJunkEmailConfiguration $_.Name -Enabled $false}
In addition, if you configured any 3rd party spam filters, which will also lead to the mails go to junk folder like the scenario 1 list here: Manage mail flow using a third-party cloud service with Exchange Online
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