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I had this problem on my new MBP 13. I opened up the case to figure out what the problem was....

Basically, there are a large number of collapsible bronze "pins" on the motherboard. Their purpose is to make contact with the bottom casing and absorb the shock of any impact so that it does not damage the motherboard.

For some reason, one of these pins in my machine was making a terrible clicking noise every time it collapsed (basically anytime i picked up the computer).

The solution I found was to stick a little soft adhesive piece of foam on the bottom aluminum plate, forcing the pin to stay collapsed. That solved the issue. You'll notice several pieces of similar foam like objects on the bottom case that perform the same function.

Are these pins viewable on the ifixit disassembly pics?
 
\Bump

I just took delivery of a brand new MacBook Pro 13" and this was one of the first things I noticed. If you press gently on the center of the bottom plate you can clearly tell there is a gap between the bottom plate and the internals. I realize this post is somewhat old but wondered if there were any conclusions? Is this by design to protect the internals or is this a quality controls issue? I was considering running to my local Best Buy or Apple store to check out their display models but figured I would see what anyone on here could offer first. Thanks in advance!
 
Your internals shouldn't be touching the case. If you take it into the store for repair, you'll be looked at funny.

It's normal, and as long as you don't set your laptop on a pole for long periods of time nothing should come out of it.
 
This is normal, you or no one else who owns a uni-body Macbook should be concerned at all.
 
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