React 16 bundles now use rollup as well; this means some of them may contain aliased requires, which will clash with the ones generated by the local rollup.
Example:
React 16.0.0.0, node_modules/react/cjs/react.development.js

var objectAssign$1 = require('object-assign');
var require$$0 = require('fbjs/lib/warning');

gets converted to

var objectAssign$1 = require$$0;
var require$$0 = warning_1;

, which is obviously invalid.

This situation could be avoided if the name candidates were tested for uniqueness while increasing the uid.
Alternatively, either the separator ($$) or the start uid (0) could be configurable in transform.js .