Wrap it up in painters tape next time, trust me. It leaves a clean edge and keeps the glass from chipping when you cut. I did the same thing on my third house, thought I was being clever with a utility knife and ended up with a cracked pane. A good razor scraper with a sharp blade makes all the difference too, no need to jam it in there. You might also try a thin putty knife to break the seal before you start cutting, saves a lot of headaches. Have you tried using a heat gun to soften the old glaze first?
12 windows and a screen door, man, that's brutal. I feel for you @reese_hayes71 because that painters tape trick sounds like something I wish I knew before my own close call last spring. It's real easy to mess up when you're just trying to get the job done fast and a sharp blade gets away from you.