Good mail going to Junk mailbox

Frequently and inconsistently, emails are being sent to the Junk mailbox. I have set rules for these emails, but they still end up in Junk. The emails that get sent to Junk are subscribed that I have created separate mailboxes for and set rules to send them to their individual mailbox. This works fine for most emails, but for some bizarre reason, emails from senders beginning with the letter M (e.g. Military.com, Medium Daily Digest.com, etc.) go inconsistently haywire. If I click on the email in Junk and use the "Apply Rules" command it is transferred from Junk to the appropriate mailbox.

At what point are the rules applied? How can I keep this from happening to good emails?