The 'close' button which appears on the pop up when clicking on notifications is missing. You've to guess it's location to click on the close button. Reproducible: Always
Works fine for me. Screesshot, please.
Created attachment 78174 [details] The close button is missing. You've to guess it's location.
Works fine on Kubuntu 13.04 beta with KDE 4.10.1
Check your screen shot very carefully, I did see a very tiny x in the right of every notification. So it is not notification error. But the theme do not work well here. Is this standard Oxygen theme? Could you try a lighter theme instead of dark theme.
And do you set transparency your self. Reset it if you do, change your background image may help too.
This was another theme problem, with BT/Glass However I'm not sure if this's the theme's fault or KDEs, cause it worked for 4.9.
Kwin is under active development for QML and wayland. Because of it, the theme api changes and will change in the future. Those third party theme should be adapt to new api.
Status changed to resolved as this is problem in theme and not problem in KDE.