Even though you say your filters are correct, it's still possible one of them is catching more than you intended.  Do ANY of the filters delete messages?

Do you access your account with an e-mail client (Outlook, Thunderbird, Pocomail, etc), phone, notifier, or any other add-on/tool/web-site/etc?  Is anything enabled in Settings->POP/IMAP?

Check Settings -> Accounts and Import -> Change Account Settings -> Other Google account settings -> Authorizing applications & sites.  Have you given account access to any other web-sites or utilities?