Google Chrome added a system menu item for its notifications a while ago. A bunch of tutorials are avaible about removing it, but I haven’t found one that is up-to-date. (Chrome renamed the flag at some point.) The solution is simple: go to chrome://flags/#notification-center-tray-behavior, switch the behavior to “Never show”, restart Chrome, and move on with life.
Edit: At some point this option was moved. Now, click on Chrome -> Hide Notifications Icon. This setting is thankfully easily accessible now.