Not being an appliqué expert, it is hard to say, but it kind of looks like the appliqué should be stitched down with the quilting surrounding them. I agree with you when you say you feel the appliqué should not be so obvious, but I think if you hand stitch them with a delicate stitch, they would look much better than machine stitching them, or letting the quilting secure them. I love your turtles, and because they are so special and well done, I think they are worth a little extra work!
Edited to say: I have searched high and low for the boo boo and can't find it??