Mail picking up old messages and marking as new

I hope someone can help - I have this really annoying problem and I have no idea how to stop it from happening.
Every day my mammal picks up a handful of old emails from a few weeks previous and marks them as new messages. Every time this happens I need to scroll through my inbox to find the offending messages and delete them again. Sometimes they are just junk messages that I have previously deleted and sometimes they are actual emails that I have read and want to keep in my inbox. My email comes from hotmail. this problem started some time ago before I updated to Yosemite and it is still happening even after the update. I've tried looking into mail settings to see if I can find a solution but had no luck. It's driving me nuts!
KRB

Try rebuilding the mailbox. This can take awhile if you have a lot of mail.
Rebuild mailbox
If that doesn't work, try re-indexing the mailboxes. This can take awhile if you have a lot of mail.
Reindex messages Mavericks/Yosemite

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For POP accounts, you can select remove from server under the advanced tab of the account.
Apple support article with information on receiving a message more than once:
Mail Problems

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Try trashing this file first, then logout/in...
/Users/YourUserName/Library/Preferences/com.apple.mail.plist
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Hello there Ibent50,
If I understand correctly it sounds like you are wanting to delete some messages or whole conversations on your iPhone. This page from the iPhone User Guide should help you do that:
Manage conversations - iPhone
Delete a message. Touch and hold a message or attachment, tap More, select additional items if desired, then tap .
Delete a conversation. In the Messages list, swipe the conversation to the left, then tap Delete.
Thank you for using Apple Support Communities.
Cheers,
Sterling

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Mail picking up old messages and marking as new

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