The Milestone future in Zoho-Projects does not work properly. 

Please take a look at Microsoft Project and see how they use Milestones. It's a much better way:

There the milestone come at the end of a series of tasks and can be made a dependency. I.e. the milestones is only reached once the last task required for that milestone has been completed.

Is there anyway you Zoho can re-configure the milestones to work like in Microsoft Project?