Tested on Samsung Galaxy S, Android 4.2.1 (Jelly Bean), CKEditor 4.0.1 samples for the Standard preset, replacebycode and inline samples.
After a toolbar button is clicked, editor dialog windows seem to open in a pre-determined place on the page, outside the editor window, and with a zoomed-in page it they are out of sight for the user. From the user's perspective it looks like something is wrong: the page becomes grayed out, but he/she needs to zoom out to see the dialog window.
It looks like the dialog windows are centered on the page or opened with a pre-determined offset that ignores the zoom level.
What is more, they cannot seem to be moved. Holding the title bar and dragging it does not do anything (it actually scrolls the page). The page below containing the editor is still scrollable. The only thing that seems to change the location of the dialog windows is zooming in and out.
This can also be reproduced in inline mode.
In Firefox 18.0.2 and Chrome 18.0.1025469 the dialog window moves around the page, too, and its location is also affected by whether the virtual keyboard is open or not.