This is a longstanding but thankfully infrequent issue. It was seen a lot when there were issues with the emoncms mqtt_input but since that issue has improved this consequential one is less prevalent, but still a pain when it does occur.
I have more recently opened an issue on github but it hasn’t attracted any attention as yet.
If you need to, you can use the emoncms/input/clean api to remove all duplicate inputs in one go, to facilitate that option I always make sure I have at least one process on any valid inputs, even if it’s not used as the api call deletes all inputs without a processlist. Unfortunately this isn’t a cure as you still need to be a aware the duplication has occurred (eg feeds stop updating) to alert you to use the api (or automate it via nodered etc)