We recently had the same problem here: Are there any known pitfalls resulting in conflicting geometry ids (geometry.id)?
It seems this issue only happens with TypeScript. I’ve provided a sample repository at the end of the linked topic that demonstrates a project setup with JavaScript and rollup that produces a build file without duplicates.
Still, it’s somewhat unfortunate that this happens with TypeScript. Unfortunately, I’m not using Typescript so I’m unable to explain why three.js gets included twice.