TypeScript transpiles a class to its ES5 counterpart, but this way it’s necessary that entire class hierarchy is transpiled to ES5.
In case parent class is untranspiled (native class or imported ES6 class, including the ones that were transpiled with Babel), this won’t work, because TypeScript relies on var instance = Parent.call(this, ...) || this trick to call parent constructor, while ES6 classes should be called only with new.
This problem should be solved in Node.js by setting TypeScript target option to es6 or higher. Modern Node.js versions support ES6 classes, there is no need to transpile them.
The same problem applies to Babel.