@Anonymous Thanks for reaching out to Microsoft Q&A, apologize for any inconvenience caused on this.
Since both Function App and App service are residing in the same app service, if we scale out the WebApp to some N instance which is nothing but scaling your app service plan to those N instances so both function App and Web App will run on those N instances.
Scaling is designed to make sure that your application is running even in peak traffic time by increasing the number of instances of your application to handle the different incoming requests, by using this same request won't be handle by newly scaled instances and it will not create any duplicate records in MongoDB.
Feel free to reach back to me if you have any further questions on this.