When you charge this sort of device, as I understand it, there's a 'trigger charge' point. In other words, if you plug it in, and it's below that point, it will charge until full. If you plug it in and it's above that point, it won't charge. I gather that if it sits, plugged in, but otherwise working, the charge can fall down to the trigger point. It's not like it automatically replaces every electron used with a new one from the wall.

It waits until the charge level is down a bit. SO. . . it's possible that you just happened to look at it when the charge had dropped -- and if you had WiFi on it could have been checking for content, etc. -- and had reached the 'recharge now' trigger point.
Also, you said "WiFi" but it will use more power if trying to connect to 3G. . . .many people say WiFi when they mean generic Wireless and vice versa, so I'm just making sure that we're talking about the same thing. So, if your Kindle has 3G, and you left wireless on, it might have been trying to get a 3G connection.
One other thing that can trigger battery usage is if it is indexing books or other content. Did you maybe recently download a bunch of stuff? It is possible that one of the files has a problem and isn't indexing properly. Here's how to find out:
Go to home and search on a nonsense string -- something you know it won't find. See what answer it gives you. If it says 'not found' and shows 0 items not indexed, you know you're good. If it shows some other number of items not indexed, I recommend giving it an hour and trying again. If it has not gone down, that's a sign that there's a problem file. Click the link showing how many are not indexed and page through to find the book title that's grayed out. Go back to home and delete that book the usual way. Then you can let it finish indexing again. Once it shows everything indexed, try re-loading the problem file. Chances are it'll be just fine the second time, but if it continues to refuse to index, contact Amazon (assuming it's an Amazon file).
Oh, one other thing: if you perform a hard restart, that will likely trigger the Kindle to re-index everything. I'm not sure if it re-indexes if you restart via the menu, but I would suspect so.