Good afternoon tmmirza,
Welcome to the Apple Support Communities!
I understand you have created one or more folders in the Mail app on your Mac and some of the messages that you move from the Inbox return to it Can you provide a little more information about the issue?
- When did this issue begin?
- When you see this happen, does the email message remain in the folder it was moved to, but a duplicate appears in your Inbox?
- Is this happening for one specific email account, or are the 20-30% of messages spread out between several accounts.
- What email accounts are affected? (Don't provide the complete address in this public forum. Just what is after the "@" sign.)
- Can you confirm whether or not the affected emails are from an IMAP account?
Create or delete mailboxes in Mail on Mac - Mail User Guide - macOS Catalina 10.15
Please reply to this thread with the information requested and I'll do my best to help you with this!
Take care.