same as any job, it depends on what the issue is?
these can always be tricky points if its a matter of policy, sometimes by not objecting to changes in the new rules, you automatically agree to be part of it.
If you have specific problems with changes, you need to raise the issue based on the fact that you signed a contract under certain conditions.
Again it depends what you are objecting to - if its a pay thing then you can argue, but if its a university policy, you'd be wasting your time.
Although from my experience when the university changed the policy on pay for our demonstrating against our original contracts, we argued the point but it made little difference because you need to get everyone to argue there is a problem, and that is pretty hard to do.
it really depends
I would suggest really thinking long and hard about whether you can work round the problem before running in shouting and screaming about policy changes though