Steps to reproduce:

1) create empty JavaFX project with main script file with run(args: String[]) function (no class)
2) create empty class named A in file A.fx in the same package
3) put code:
      var a = A {}
      a.foo();
   into run function
4) Alt-Enter on line "a.foo();" and select "Create function foo in A"
5) function foo() is created in main script file instead in A.fx

NB 6.9 beta with bundled JavaFX SDK.