Alfred doesn’t see Simulator app

One thing is speed. I believe Alfred is currently faster than Spotlight. And, this is specifically for Lion I believe, Alfred learns where Spotlight doesn't.

If I want to launch Adobe Photoshop and start to type 'Ph' Alfred will offer Photoshop as an option and move it to the top with the more I select it.

With Spotlight, Photo Booth with be the first choice, and it will not learn what I want with repeated use. I believe at one point it did, but lost the ability in Lion.

Your Spotlight index might be corrupted – Alfred uses the same index as Spotlight.

If Photo Booth is the only item missing, you can try dragging it out of /Applications (to your desktop, say), then back in. You’ll have to authenticate as an administrator both times; Spotlight should pick up on it after that, and so should Alfred (after a small delay). If that doesn’t help, or other items are not found either, you will have to re-build the Spotlight index, either by following Apple’s official procedure, or via the Terminal command sudo mdutil -E /.