Sometimes the berry can be pushed to the back, but can be nudged forward. Not all patterns will tell you to do this, but where your berry, bobble or nupp is made, the stitch into which all your increases is made can become stretched out, and thereby swallow the berry. If you knit into the back of the stitch, this tightens the stitch you are knitting into and can prevent it from disappearing to the opposite side.
There is another trick which is to pull up a loop to close up the whole berries and bobbles make on the reverse side with a crochet hook and then K2 TOG. It is best to do this on the row right afterwards.
Also, if you make your berry or bobble looser, there is more yarn used and this also helps keep it on the front side. If I got too far away from the bobbles and then noticed the problem, there is sewing them in place from the backside so the front side looks good, in the meanwhile the first two suggestions may help you.