My wife's 2011 has just started doing this about a week ago, figured I'd jump on the forum and do a search (been off of here for a while, life is way too busy lately). Imagine my surprise to find a current thread talking about this exact same thing!
For ours, it appears to be related to regen. If you let off the accelerator and it goes into regen mode (2 or more bubbles) then I get a click, then back to accelerating I get another click. One click each way, not both. I can get it to happen by lightly tapping the breaks, or just letting off the accelerator. Also noticed that it doesn't happen (or at least not nearly as noticeable) when I have a full charge, meaning that it's not going into regen because it doesn't need to. That's the case even when braking, which leads me to believe it's NOT a brake issue.
By the way, it's MUCH easier to hear things like this when you're in a garage. The concrete walls bounce the noise back, so things you might not notice out on the street can be very obvious in an enclosed garage. This clicking is definitely loud enough to hear out on the road even with the windows closed (when I turn down the stereo, that is), but is much louder in the garage at my work and makes it obvious that it's NOT normal and definitely wasn't there a month or two ago.
My wife's old Prizm (her gas car before the Leaf) had a similar problem, and it ended up being a loose motor mount. The whole engine was basically shifting back and forth when it went from compression to acceleration. I'm wondering if it's something similar with something being loose so there is a little play when the rotation direction switches or something.
Very curious to see what comes out of this thread. I'm trying to figure out when I can take ours in to get it checked out, but like I said life is crazy so hopefully I'll get some answers here which can save me time at the dealer!