I've found a way to reproduce it reliably.
Stand next to a staircase or other exit and press F5 to quick save. The saving spinner should start running, and shortly after it's finished you should see the notification about the save being successful.
Then press F5 again and exit the area after the saving spinner stops, but before the notification pops up.
When you arrive in the other area, you won't get the notification, and all future notifications will be queued but not shown until something happens that fixes it, causing the game to flush the queue like notification diarrhea.
Not a game dev myself, but I don't think it should be too hard to fix.