Intermittently unresponsive keyboard and trackpad on Macbook Air
I would create a new user and see if the behavior happens under a new account, so you can isolate whether this is System Wide or just related to your own account. Check your Launch Items in system preferences and remove everything just to test. 

How much free space do you have? For what is worth, I'm using a MBA 11' mid 2011 and I have the same behavior sometimes when Arq2 starts and I have IntelliJ + Xcode running. Like the CPU is under a lot of "pressure" and I totally experience the same. It lasts a few seconds (10 sometimes!).

So I doubt there's anything to do, unless this happens very often to you, in which case I'd take it to an Apple Store for either reinstall or some hardware check.