Hey Naveen! Julianne from Mixpanel Support here.
Are the custom events newer? If so, it does sound like expected behavior. The Flows doc goes more in-depth, but at a high level Mixpanel automatically considers the most used and common custom events in your project, displaying them in intermediate steps instead of showing the underlying events. If a custom event isn't commonly used, you can use it as an anchor, but it won't show as an intermediate step.