Seems to be a combination of OS X 10.8.4 and LLDB. As kenster says, switching to GDB makes the problem go away.
Edit:
It’s caused by a race condition in the debug server (I hear).
Here’s a fix if you want to keep using LLDB: Instead of clicking Run while the app is already running in the simulator, kill it in Xcode (⌘-.), say “I love Xcode” 5 times and Run it again (⌘-R). It won’t crash, I tested it.
Fixed in Xcode 4.6.3.