Beth Brown-Reinsel published a wonderful tip in her newsletter. It is simple to do and can be done after the knitting is completed.
For each bobble, use a crochet hook to pick up the left side of the stitch next to the bobble on the right. Pull the thread on the crochet hook over the bobble, right to left. Then pick up the right side of the stitch next to the bobble on the left. Pull this thread over the bobble, left to right.
You will be amazed at the result. The bobbles perk up and don't even try to slip through to the wrong side of the work since they are held in place by the sides of their neighbor stitches.