These machines are crafted using the highest level of precision in the industry.
It sounds as though one of the three locking points isn't being properly aligned when you close it, or one of them has a faulty construction--and I'd bet on the first being the real problem.
When you close the bottom cover by rotating it into place, the three pins and sockets on the inside of the cover all lock into place. It sounds like one of these has not been seated properly when closing the cover into locked position.
Check carefully that you are closing it properly, and take advantage of your free AppleCare telephone support so they can explain and verify if there is a mechanism problem.
But this is NOT common nor acceptable, because like I said, all the pieces of this machine have been precision designed and manufactured to have absolutely no gaps and perfect fit and finish.