Now that you have a bigger instance, space should not be an issue. Please, check that all services are running by executing:
sudo /opt/bitnami/ctlscript.sh status
That error is really weird. Is the file there? You should obtain this result:
$ ls -larth /opt/bitnami/apps/magento/htdocs/bin/magento-cli
-rwxr-xr-x 1 daemon daemon 472 Oct 23 06:47 /opt/bitnami/apps/magento/htdocs/bin/magento-cli
Could you verify if the script is there and if permissions are correct? Also, running support tool again could be useful to get the latest information.