Are you saying "Alexa stop" in a continuous phrase?
I find that if the device is busy doing something like an alarm or timer, it is better to say "Alexa", and wait for it to drop the volume (as it will), then say "Stop".
I've actually enabled the beep on activation, and I find it helps a lot (Sounds and notifications, Request Sounds/Start of Request. I don't use End of Request, as I find it confusing.)