Mail.app moves back e-mail to inbox

Hi
I used to use outlook for OS X, but after successful upgrade to Yosemite I decided to move to mail.app. I constantly experience that all mails in my inbox (I have two accounts which is showed in the Inbox) which I move to folders, is suddenly moved back to the inbox. Its quite annooying to get all my read and stored e-mails back in my inbox view, so I have to move them again.O anyone have a solution to avoid such behaviour in mail.app?

What kind of email account is this—IMAP, POP, Exchange? If you have more than one account, are they all affected?

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