When using a custom a custom rollup config, it gets loaded with require in util.fillConfigDefaults and the dest property is set on this config object in bundle.runBundle. This works fine the first time. When bundleUpdate is called from the watcher, the same instance is returned by require and the dest is set like this in bundle.runBundle:
rollupConfig.dest = join(context.buildDir, rollupConfig.dest);

Because it's always the same instance of rollupConfig, this will append to the dest with each watch trigger, leading to wrong paths.

See a detailed post about it here with screenshots: https://forum.ionicframework.com/t/having-a-custom-rollup-config-breaks-the-watcher/65343