Just weird that it would say "Not charging" but actually be charging.
It works like this. A normal, fully standard USB port can supply 500mA of power (2.5W).
An iPad mini usually uses about 1.7W-2.2W while you're using it. It will tell you that it is "not charging" because the power you're draining while using the iPad is basically the same as what is coming in through the computer. Almost nothing is going into the battery. I don't know what the exact cutoff is for Apple, but it looks like if the battery isn't getting at least about 1W, it will display the "not charging" message.
But as soon as you put the iPad down and it goes to sleep, that full 2.5W goes into the battery. It will slowly charge the battery until it's full, about 7-8 hours from empty on a normal USB port and about 3.5 hours on the included 5W power adapter (or on a compatible Mac with high-power USB ports).