You come at a certain point in the development of every app that what you see in the simulator does not match what you think should happen. Mostly these are human errors --
If you select Clean from the Product menu, XCode will delete the files inside every folder in the Build folder, if you select Clean Build Folder it will delete the entire Build folder.
After Clean command:
After Clean Build Folder command:

I think you should select Clean Build Folder when you want to build a binary that you want to release to the AppStore, when you messed up with your project or when your app doesn't work for an "unknown" reason, otherwise use Clean.
I hope I've answered your question :D