Microsoft project management software used to plan, manage, and communicate a project schedule and other information among workgroup members, project managers, and other stakeholders.
Theuns Eloff,
Project ("it") is not doing it, you are. If you are expecting Project to have intelligence that says, "hey, you can't show progress on a task that has a FS dependency", then I'm afraid you are asking too much. Project has NO intelligence, it responds to inputs by the user, whether they make logical sense or not.
Project will catch some scheduling issues (File > Options > [schedule warnings, planning wizard, etc.]), but it can't inject thought into the process.
When a plan is developed it may indeed be true that task 1 must be completed before task 2 can start. However, things can change, perhaps the dependency was not hard (i.e. some part of task 2 can in fact start before task 1 finishes), or maybe the dependency wasn't valid at all. That's part of project management, creating a plan, statusing the plan, and adjusting the plan as reality prevails.
Hope this helps.
John