Apple cannot stop someone from making a WhatsApp account with your phone number. It sounds like you have a problem with Meta, that also includes Facebook. If Meta does not want to assist you in preventing your account with them from being breached, I would suggest to not use any of their services.
Just because an app is available in the App Store, does not make Apple responsible for that company. Just because you can order a product from Amazon in an app, does not mean it is Apple's fault if the product is delivered damaged. In all cases you need to talk to the owner of the app. As far as Apple's interest, you should know that there is absolutely no income for Apple when a free app such as Facebook or WhatsApp, is downloaded.
What it really sounds like is happening is that you are a victim of a phishing message/email. Someone contacted you claiming to be someone else and you inadvertently gave them your sensitive information. Apple or no other company is able to stop you from telling someone your Passwords. The best way to solve that problem is to NEVER click a link or call a number provided in a message/email. Stay off Social Media as they are just a cesspool for scams. An here are more tips and suggestions for reporting these messages.
Recognize and avoid social engineering schemes including phishing messages, phony support calls, and other scams - Apple Support
Creating a WhatsApp account will not give someone access to your Apple Account. To check if someone is logged into your Apple Account, go to Settings > [name on top], and scroll to the bottom to see the devices that accessed your Apple Account. If there are any you do not recognize, tap to remove them and change your Apple Account password.
Change your Apple Account password - Apple Support
