I've had it happen, and from what I've read and been told, it's a bacterial bloom. It usually happens after a really good cleaning of the substrate, and you've disturbed a pocket or two of organic waste which causes the bacteria to briefly overpopulate. It usually goes away in a day or two as the bacteria consume all the waste and die off.
If that's what it is, it's harmless, and can be prevented by making sure to clean the gravel well every time and don't overfeed.