iosmail.app
I'm using Mail on iOS with an IMAP account. When I flag an email and choos "move to junk" the emails disapears from my inbox. After syncing the account again the email is back in the inbox.
Checking the inbox at OSX shows it marked as spam and it's still in the inbox.
How can I make Mail on iOS doing what the label states: Mark the email as spam and move it to the junk folder?
Mail.app has a feature called rules that enables you to automate your mail tasks.
You can define rules in the Mail preferences.
It seems iCloud is marking the message as junk using its algorithm. I don't believe you can adjust this from within the Mail.app. You will need to log into iCloud.com, enter Mail, find the particular message in your Junk Mail folder and then with the message selected, select the gear menu and you should be able to Mark as Not Junk.
To recap, as iCloud is flagging message as junk you must unflag message within iCloud.
Best Answer
I'm not at all sure this will work for you, but since nobody else has responded...
I set up a manual email account yesterday on both Mac and iOS, and my ISP warned me that both on Mac and on iPhone I needed to add "INBOX" as the IMAP Path Prefix in the Advanced Settings for the account, or else I would have trouble moving messages from Inbox to Trash and Junk. I was having a similar problem moving messages to Trash, and that did the trick. You might give it a try, since it's easy to undo if it doesn't work.