Strange...I'm having the same issue. I ended my cycle about a week before I started the diet. On day three of phase one, I noticed the bloody discharge. Its been occurring for three days now. The first day I noticed it...it was very light, but the next day, the discharge was more like what you would experience at the end of your cycle (during the final spotting phase, only I didn't actually spot). Today, I noticed the discharge was no longer fresh looking (as in, fresh blood)...now the color has changed to a reddish-brown and the discharge is much lighter.
I'd be interested to know if this is a common side effect, and if so, what causes it.