Vinyl can be a real PITA! Did you use water on the trunk lid and on the vinyl when you installed it? I just replaced my magnetic strip with vinyl and I had some bubbles too. I was able to work them out with the hand squeegie and patience, but that was when it was still wet. My bubbles were water pockets that would ooze out when I worked it from center to edge. It may be too late for you now to work them out though. You may want to call the vendor you got them from for advise! Good luck!
Click on my sig pic for Big Red's build journal!