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Hi. I just update Android 6.0 on my Xperia M5 and my camera, gallery, contacts and so on, he incerases permission ''screen overlay'' and ''for this settings, first turn off screen overlay from Settings>Apps'' and i accessed the settings and apps, but i was sent in ''Draw over the App'' or something and i couldn't turn off the screen overlay. So i can't use all the app;icationsin detail. What can i do? Please help me quickly. Thanks. 
I have the same issue on Z2 since update to marshmallow also the new stamina mode too so ive reflashed back to lollipop. marshamllow is the worst update ever..
I have the same problem with Xperia Z2. I'm so frustrated -- I've spent the last few days trying everything, inlcuding a Factory Reset. What's more, before all this, my back/home/recent apps buttons no longer work, so I need to use a third-party app to get those important functionalities. Otherwise, I have to turn the phone off every time I want to use a different friggin' app!!! With the third-party app, I could at least use my phone, but this so-called security update has rendered my phone completely useless -- might as well have a 15-year old Nokia. I'm betting that the Screen Overlay error is caused by the third-party app that I have to use in order to actually use my phone normally!!!!! By the way, I don't have Lux, Clean Master or Facebook Messenger, Twilight installed.
Might as well throw this $500 phone in the toilet.
I haven't given up all hope -- though I am pretty close to giving it to my 2-year-old daughter to use to watch Youtube videos, as that's pretty much all it's good for at this point.
Perhaps I'lltry reverting to Lollipop. Any other ideas?
Not sure why but I uninstalled Clean Master and the error message stopped coming up. The issue is probably with this app.
Hope this helps everyone.
I'm also observing the same issue in M5 dual.