I have had this same thing happen to me. I was told I over stirred the isomalt and shouldn’t have added the color after I took it off the heat. I was told to add the color while it was on the heat so the bubbling of the isomalt mixed in the color. Then you wont have to stir it more to mix it in. Key for me has been less stirring the better. And I use a bakers torch to pass over the isomalt for a second to get ride of any cloudy look or air bubbles.