I've had a problem with Xcode 4.3 and 4.4 where it will not quit after stopping the simulator. The problem is that Xcode thinks that tasks are running (even with the simulator not running). The only solution is to force-quit Xcode, which is a pretty major interruption in your workflow.
Here are some threads that appear to talk about the same problem:
Failure to stop executing task in Xcode 4.3
Why does Xcode 4.3.1 (4E1019) / 4.3.2 (4E2002) hang regularly with iOS simulator?
My 2 XCode 4.4 problems
I haven't found a workaround so far. The last thread on cocoabuilder.com indicates that you should add some extra logging to find the problem:
defaults write com.apple.dt.Xcode IDEDebuggerLogToFile ~/IDEDebugger.log
Update: the problem seems to occur less, when I quit the task from Xcode. Normally I'd just punch Alt-Q to quit the simulator altogether; now I alt-Tab to Xcode first, then punch Alt-. (Alt-period) to stop the running task.
Update 2: I found a suggestion to clear the project from the organizer window: Xcode 4.3.2 process hangs.
Update 3: It still happens, even with Xcode 4.6... There's another suggestion that says to click the Simulator icon in the dock, which seems to work for now.
XCode 4.3.2, issue with running on simulator
This is my pet issue, and since this is the internet, every time Apple releases a new version of Xcode, I will loudly point to this bug and ask Why haven't they fixed this??!?!?!!111!! When they do fix it, I'll still keep using it as an example why Xcode is "broken".