Glad to say that I have found a solution for this problem.
The user was using Samsung S10 Phone and 'Email' app on the phone as email client. By mistake the user selected one of the internal email and marked is as Junk. Because its a Samsung App, the rule stayed in the Samsung App on the phone and not transfer to outlook cloud we could not see this rule in user profile in exchange admin. This also caused sporadic movement of messages (sometimes message stays in inbox for hour or other times few min) By deleting this rule would solve this problem but if the problem persists then follow the steps below.
If anyone user facing a problem where email is coming in to InBox then moving elsewhere in the information store then
- Delete all Email profile from outlook, mobile phone tablets and any other laptops or devices user own.
- Using the webclient, delete all user rules (you could backup the rules before)
- Using Webmail at office.com check if the message is still going in to junk/spam folders
- If it is then use MFCMapi to delete the junk rule from the list and check. Link to show how to delete rule: https://learn.microsoft.com/en-us/exchange/troubleshoot/administration/delete-junk-email-rules-mfcmapi-exchange
- Ask the user to login to webmail and If email has stopped going to junk mail then re-create a new profile in all devices.