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This happens to me quite frequently. The back button, top and bottom stuff on my phone will disapear, Sony Xperia Z1 with the latest update availiable. i will provide a screenshot.
It takes lots of restarts to finally get it all back to normal and its very annoying
Will also add, when i lock or turn my phone on, the lock screen will not appear, it will go straight into the phone, and when i open an application i cannot go back, or get back to home page without restarting phone
Repair your phone with SUS, make sure to backup everything on your phone before you do so
Bridge (for Mac)
Alternatives on How to backup Xperias