Crystal Bubbles have a chrystal shield that have to be broken to make the crystal bubble into a normal coloured bubble. You break the shield of a Crystal Bubble by bursting bubbles nearby the Crystal Bubble. When you have broke the spell to the Crystal Caves, you are introduced to Crystal Bubbles at level 86. Good bubbling!
You can find a list on where Crystal Bubbles can be used in the topic on Special information about Charms at GU!