Please post a few pictures for better understanding the issue. What type of glass are you using (soft/Boro)?.
I believe it might be the heat you're applying to the piece is not good enough to melt the whole piece, It's happened to me a few times; also, are you somehow shaping your pieces?, for example using molds or graphite tools?, sometimes they leave unperceptible wrinkles (when heat) and when they cool down you see them.
Sometimes when applying color you have to be carefull not to burn out the color, some like reds and yellows are pretty delicate, it's better if you hit them on the farest portion of the flame first and then move into the center.
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