First, you'll need to be sure if you're transmission was damaged or your clutch. Second, you'll need to prove there were no issues to begin with. Third, since you claim you could not drive your car after emissions you should have record of it being towed from the emissions location to either your home or mechanics. Last, contact the department to find the process in which to file a claim and include all your proof including who worked on your car at that station.
If you left their property before having a report filed then they are likely released of liability.
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