Yeah, if it's just a log, it's an informational message logged to the console... I guess at least you narrowed out the possibility of it being a JS error for you. But strange that I don't see the issue with iOS5 on an iPhone *or* iPad (always works with 1 click for me).
I actually caught it doing it once for me as well yesterday. It was a time that I didn't have any alerts and I saw the same thing, click it and the tab highlighted with the normal blue and saw the AJAX graphic in the upper right. When the AJAX graphic disappeared, nothing happened with the alert menu (although the tab stays blue).
I have a feeling it might be a timing issue, which is why you only see it once in awhile. iOS has no way to know if you are "hovering" above an element until you click the screen. So the click is firing both the hover AND click events. I haven't dug into the XF code, but maybe the click event is canceling the hover event... and if that's the case, maybe it's choking if the first AJAX request made isn't returned until after the second one is? Just a theory anyway...
Yeah, I wondered it it wasn't somehow triggering the event to open and close somehow so fast that it appeared it needed two clicks to open when it was really happening, just too fast, and the second click re-opened it? I might be confused on how the alert notification opens, though.