What do you tell customers when the fob is programmed, but works every other time?

I have had two cars come back to me this past couple weeks after programming a key fob that only works every other time you press the button. (Toyota and Honda)

The customer will come back and state that it stopped working. Both times, the fob was working and programmed but just takes a couple of times pressing the button. I’ve changed batteries, replaced fobs, reprogrammed and still have this issue. Am I missing a step here in the process of programming? Is there something faulty/worn out on the car that caused this? Allegedly, the Toyota I had these issues with had a new car battery as well.

If it is without a doubt something in the customers car causing the issue, what’s the best way to go about politely explaining this to them? Yes, we have them sign something stating that we are fixing their car fobs, not oil and engine lights, before we attempt to program. I imagine most people sign without reading that, so what’s a polite way to convey that to them after the fact?