Breakthrough bleeding is common. and a pain in the butt.
I was on the protocol for 9 months last time. I finally stopped and started pumping, even though we had no baby in sight, because I was tired of dealing with the breakthrough bleeding.
It will get better, but it will be back. Everyone is different, and there's really no way to know when it will stop. I always wore a pantyliner, as I never knew what was going to happen.
I had a full supply for ds, though, so it was totally worth it.