The code is setting up an action to perform (Arg.Do) after the calls have already been made. I think this is what you are after:
List<B> args = new List<B>();
IA a = Substitute.For<IA>();
a.MethodA(Arg.Do<B>(x => args.Add(x))); // do this whenever MethodA is called
new MyLogic(a).DoLogic();
a.Received(2).MethodA(Arg.Any<B>());
Assert.AreEqual(2, args.Count);