Hello @Mohamed Roushdy , Welcome to the Microsoft Q&A forum.
Azure Application Gateway deployed with availability zones are by design deployed with 2 instance counts to maintain high availability. When Application Gateway scales the instance counts are evenly distributed within these availability zones.
In your case above you should choose minimum instance count as 3, so that each instance is deployed in an Availability Zone.
Hope this helps! Please let me know if you have any additional questions. Thank you!