Could you please click on my name and send me a PM with more information about the contract you are referring to? I will be sure to look into your report and respond to you accordingly.
You should insist in creating one contract and under one contract you can create several milestones. Creating several contracts for ONE JOB, will limit your options of disputes.
If you create different contracts, then yes, you are right, they can change ToS of other contracts and you will not be able to disputes because you can dispute milestones in one contract. You cannot dispute or relate disputes in other contracts.
Your app development team are trying to play safe and smart with you, so you will not have lots of options when you will have any disagreement with them.
Better to stick with one contract and make sure you will release milestones once they completed.