What a cute quilt!
I use the glue method all time for binding. It sounds like you may have used a little too much glue or your placement was a little off.
I always fold and press my binding to the back once it is stitched on the front. This way, I am sure that I will cover my stitching line. It also makes it easier to see where I need the glue - I usually apply it right above the stitch line.
If it doesn't work for you, then you just need to find a method that does!
:)