So here are some screenshots.
First on shows browser (Firefox) not running in full screen mode at standard zoom level (Ctrl+0):

The souce code popup extends beyopond the bottom of the browser window.
Next, in this very state, I zoom out, i.e I press Ctrl+- twice and the Apply button appears:

Next, I close the source code popup, then press Ctrl-0, followed by one Ctrl+-, i.e. from standard zoom level, I zoom out once, then open the source code popup:

Notice that the Apply button appears partially at the bottom. Also note that the top left corner of the source code popup is placed far more to the top of the browser window. Completely different calculation results, it seems.
Next one is the same as the previous, except that from standard zoom level. I pressed Ctrl+- twice before opening the source code popup.

Next, I go back to standard zoom level, then switch the browser to full screen mode, and then open the source code popup:

And finally, I zoomout by pressing Ctrl+- once:

Apply button becomes visible.
Hope your developers will be able to reproduce that strange behaviour.