In search of the lost notification window...

Hi there,
I'm having a question regarding Mac Os X. It's a question that I'm having for many years. It's something that annoys me regularly and today I would like to find out if others have the same problem, too, or if there might be a simple solution that I'm not yet aware of.
I'm using OS X with a lot of applications open, on two different monitors and several virtual desktops. I'm regularly having the problem that I open a file in an application and there's a notification-window somewhere and I can not find it.
I'm illustrating this with the last incident, just 5 minutes ago: I've pulled an image file from an email-attachment in Airmail to the Photoshop-icon in my dock. I'm checking other emails while Photoshop is loading. I go back to Photoshop when it finished starting-up. The image-file is not open yet and all menus are greyed-out, because there's a notification-window open (probably informing me about a missing color-profile), but it's hidden somewhere behind other windows. I've programmed two of my hot-corners to show me all windows of the active application and all windows of all applications, but it does not show me the notification window if I trigger that function. Even if I'm checking each (virtual, real) desktop and pull away each application-window I can not find the notification window for Photoshop. All I'm able to do is to force-close Photoshop (because all menus are greyed-out) and re-open Photoshop and re-open the image-file from within Photoshop again, with Photoshop in the foreground to get the notification-window to show up. It's a bit annoying.
The same thing happens to me constantly when I'm copying files. Sometimes it takes 30 minutes or longer to copy large files or archives from one place to another. Sometimes I'm just losing the window showing me the copy-progress. Even in the finder-menu "Windows" the copy-progress is not shown, so I'm not able to bring the progress-bar into the foreground via the menu. All I can do is search manually through every monitor and virtual desktop by pulling away windows and looking what's behind them until I found the progress-bar-window. Sometimes I can just not find it nevertheless. If I go into one of my hot corners then the progress-bar-window is not showing up as a regular window. So sometimes, when I 'lost' that progress-bar-window and I'm not sure if the copy-process is finished or not the only possibility to check if the copy-process is finished or not is to try to eject the drive I'm copying to or from. If OS X tells me: "not able to eject drive because blabla..." then I know that the process is still running, but I won't know how long the process is still taking. I just have to wait and try again and try again and try again until I can eject the drive.
I'm not sure if I'm the only person experiencing this. Maybe I just have too many windows open, but I'm working with a lot of different files and apps. In my opinion it's a programming-bug or at least a very annoying characteristic of the Macintosh Operating System since... I don't know, maybe 2000? Or Os 5? I think it's been a characteristic of any Mac OS since I'm working with Mac, so probably since my times on a Performa ...
If someone has a tip for how to locate these notification-windows and progress-bar-windows in case they get lost: would be wonderful to learn about a work-around, or even better: if some programmer at Apple could just put notification-windows and progress-bar-windows into the "Windows-menu" where they obviously would belong to. A simple change like this would make my Mac-experience so much more efficient ...
Many thanks in advance!
x, S

Weirdly enough I can not replicate the missing notification-window to take a screen-grab: the notification window now always just stays in the foreground. Maybe it's really a bug that only happens once in a while...
If you open a file and a notification-window pops up, then activating Mission Control HIDES the notification window though. That really should be considered not to be a bug but an inconvenience that could be avoided by including the notifications in Mission Control.
Will try to take a screen-grab next time it happens...

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