I went to the Node.JS forums and asked what could be the issue. Not a babel issue at all, just circular dependencies. For example:
// A.js
import B from './B.js'
export default class A{}
// B.js
import A from './A.js'
export default class B extends A{}
Sorry there wasn’t nearly enough information to be able to figure this one out. I got a lot of help on the node.js github and someone looked through my project on github and ended up finding an instance where two modules pointed at each other.