IMO, the main reason it could negatively affect muscle growth is if it's making you burn too many calories, thus creating a caloric deficit. This is why it doesn't make much sense to me to spend money on a fat burner while bulking. You eat to create a caloric surplus to gain muscle and you eat(and do cardio) to create a caloric deficit to lose fat. If you're just using it to decrease fat gain on your bulk, why don't you just nail down your diet to the point where you can just increase and decrease calories slightly, as you see fit, to gain the way you want.
If we're talking decreasing preexisting muscle growth, the same reasoning could apply there as well (caloric deficit created, leaving muscle to be broken down as an energy source).