Did you found those holes after you had it set up and started quilting it?
If so, my first reaction would have been "oh, snap" (or something similar!!!)
Is it possible for her to see it and for you to consult with her about what to do?
The suggestions have been good. If it were mine, I would start with fray-checking the edges and then maybe do the appliques after the quilt was off the long-arm.