The special folders in Favorite folders collect messages from all accounts. If there are copies of the same message it can mean the message is copied into more folders or among more accounts.

Common causes for this include:

• Duplicate setup - make sure each of your accounts is set up only once in Menu > Accounts, or all messages will appear twice in Favorite folders
• Rules - do you have any rules that are meant to copy incoming messages? Check the Menu > Rules to make sure that there isn't a rule creating unwanted copies.
• Forwarding - do you perhaps have a server-side forwarding set for one of your accounts? If you don't want messages from one account to always be forwarded to another, check your server rules, for example through webmail

Note: In eM Client 6 this problem also sometimes happened with Gmail accounts, which keeps a copy of each message in All Mail folder and also created copies in Important and Starred labels.
Since eM Client creates a separate folder for each label, emails that have multiple labels attached to them will have multiple copies saved. The only workaround for that issue is to disable the showing of redundant labels like "Starred" and "Important" in IMAP. You can find this option by opening a web browser and logging in to Gmail. Click on Settings, and then go to the tab at the top called "Labels".

Since eM Client 7.0 we have adapted Gmail's internal structure. All messages have just one copy in the All Mail folder and other folders are just assigned labels.