I have some problems with my mail application on my phone. When I access my inbox, I saw that there were 120 mails that are unread even I read them on my mail application. I use Sony Xperia Z3 and I use the default mail application. What is the problem?
First off: Try another mail application to determine if the problem persists.
Which version of Android are you using? Try updating your Stock Firmware via OTA. Weird stuff like you are describing is sometimes a bug somewhere in the Operating System.