IMHO we need some basics in order to be able to help...
- what image are you running? the std node-red:3.0.2 from dockerhub or your own image? If the latter, can you post the Dockerfile?
- what is the command or configuration you use to launch the container, in particular, what are the volume mounts and what are the options to npm start?
- what are you trying to achieve by running node-red-stop?
- you mention SD card issues, have you deleted the nore-red docker image and done a fresh pull?
