Bettas do, and often change coloring. I doubt it was an ammonia burn since the ammonia mainly burns the gill area, and would not burn the entire body and fins of your fish. There are a few things you can check to see if they have changed from the pet store conditions, to the conditions he is now.
Tank size- Your bettas colors will be richer when he is in a larger tank. This is a sign of happiness
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Temperature- The warmer the temps, the richer the colors. Another sign of you bettas comfortability.
Food- Same thing here. The better the food, the better the colors.
There are other things too like water conditions and attention. I hope this helps!
Alexa