Stock Phone app doesn't work in split-window mode on Android Nougat
For an app to be allowed to work in split-window mode, there is a certain parameter android:resizeableActivity=["true" | "false"] that has to be set to true.

Since Android 7.0, this is true by default, but it's still possible to be set to false if the developer thinks the app will not behave correctly in split-window.

As @Andrew T. suggested in a comment, all you can do as a user is to find another phone app that allows split-window.