If you click on the menubar icon and then press ⌘Q with the GUI open, the app does't quit and the icon stays in the menubar but becomes unresponsive to clicks.
I couldn't reproduce this bug at first, but it looks like it reproduces if there's a pinentry (passphrase dialog) open at the time you quit. We're working on it!
Keybase GUI Version: 1.0.16-20160803190018+268b023
If you click on the menubar icon and then press ⌘Q with the GUI open, the app does't quit and the icon stays in the menubar but becomes unresponsive to clicks.