TLDR
I sometimes run a local vanilla minecraft server. I have experienced the problem there as well.
For me, I had tier's of water flowing from a single source in an gently slopped pyramid fashion. I was not using a dispenser, I was allowing/restricting flow with a piston. At random times a source block will be created down stream in some random water flow location.
So, the question is when and if Notch and/or his team will find and fix the problem.
I don't recall if I experience the problem in Single Player. I've pretty much abandoned that mode.