react-app is using custom option for transform-runtime, like follows:

moduleName: path.dirname(require.resolve('babel-runtime/package'))

It results in following fragment in transcompiled code:

import _classCallCheck from "/Users/sheerun/Source/Hyper/worker/node_modules/babel-runtime/helpers/classCallCheck";

but you detection code checks for:

import _classCallCheck from "babel-runtime

It makes your plugin fail with following message: An unexpected situation arose. Please raise an issue at https://github.com/rollup/rollup-plugin-babel/issues. Thanks!