I will presume you are using InputListener class. Because Input class don't have a touchUp method. You didn't mention this part in your question.
I'll assure you touchUp funciton will not be called twice. You are using an emulator, and in this case touch up function will be triggered by the mouse button. So as long as there is not a second mouse pointer(?), touchUp function is called once per click.
I also will presume you are using only one Listener.
What is happening is touchUp function is not the only function triggered by a mouse click. If you change the position of the mouse while holding it, touchDragged function will also be called. Maybe that's what is confusing you.
Try to put a
System.out.println("TOUCH UP"); into your touchUp function to be sure of how many times that function is called. And please don't put it in anywhere else.
If your problem insists on happening, please provide us with more information, so we could help you.