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I have two windows open (so far I think this has only happened when at least one of the windows is a Finder window, though I'm not sure if that fact is essential to the problem), and I click the one in the background. The previously-focused window changes shade to show that it has lost focus and the now-in-focus window also changes shade to show that it has gained focus, but no matter how many times I click it, it doesn't come to the foreground. I have to try cycling between the windows in order to successfully move-to-background the out-of-focus window and move-to-foreground the in-focus one. Why would this happen? I've never seen such behavior in older versions of OS X and don't think it's a Lion "feature" either.

EDIT: Screenshot attached showing behavior in 10.8 Screenshot of behavior

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Not going to add this as an answer, as it hardly counts as expert knowledge or hard evidence, but I have been observing the same behavior with Finder windows. I’d very much surmise this is a bug of Lion’s window manager… –  kopischke Apr 30 '12 at 22:37
    
Happens to me, too. I seem to recall it happens more frequently when one of the apps running is in full-screen mode. Have you noticed anything similar? –  John Rygielski Apr 30 '12 at 23:08
    
Interesting. I never run apps in full-screen mode, so could not comment on that; accordingly, the behavior I have seen only applies to apps in windowed mode. –  Philip May 1 '12 at 2:58
    
I'm sure this is a duplicate, but I can't find it right now... –  Max Ried Jun 14 '12 at 10:31
    
Is it something like apple.stackexchange.com/questions/42827/z-windows-position-lock/… –  Max Ried Jun 14 '12 at 10:38
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I've noticed this in versions of OS X as far back as Panther. It seems to happen more often with apps that use heavily tweaked windows (like Microsoft Office, Adobe apps, or Java apps, particularly Eclipse).

It's just a bug in the app. File a report with the vendor if you want and maybe they'll be able to fix it.

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Often the problem app is Finder itself... –  Philip May 13 '12 at 20:37
    
@Philip I've never seen Finder do that; it's usually the best-behaved app (as far as windowing goes). –  CajunLuke May 14 '12 at 0:02
    
I'll be curious to see whether I can reproduce the behavior with only Finder and get a screenshot.... –  Philip May 15 '12 at 15:13
    
So far I haven't reproduced this behavior in 10.8. I'm tentatively accepting "bug" as the explanation. –  Philip Aug 15 '12 at 19:51
    
I have reproduced this behavior in 10.8 with only the Finder. Have two folders open, drag a file from one to the other. Other folder comes to foreground, while first folder retains focus. Since it's just Finder, is it still a "bug in the app," i.e. in Finder itself? –  Philip Sep 3 '12 at 17:36
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