Lid off the master cylinder, then try pushing them in a little more. It could be that one of the pistons has crabbed, so they might need to be pumped out a little again, checked for squarness to the bores, then eased back in again. Failing that, it might be that you need to pull them out for seal replacement etc. To clean the crap out of the seal locations, I use a small pick tool. There are normally three in a set, one right angled, one oblique, and a straight one. Soak the crap first with something like penetrating fluid to loosen it up. Dont scratch the bores