Luckily this is not easy in PhpSpec, nor any other testing framework. Objects are passed by reference in PHP. If you change the reference you no longer have the object which you could compare to. You'd have to copy the original object and compare it based on its properties. Not a good idea.
Method which modifies its arguments is a bad practice in general, a bad idea at least. Usually a client of the method doesn't expect modifications. I'd rather think how to design your class better.
Your example doesn't really describe your problem very well. If you gave a better one, we could provide a better help.
If you only want to verify that a method was called on an object (as opposed to changing the reference from your example), use mocks.