Everything may depend on the exact wording to the papers that you signed when you got the car, but the car company may be able to rightfully repossess the car even if the title was mistakenly issued without a lien.
You should consult with an experienced consumer attorney. I suggest you look for one at www.naca.net. An experienced attorney may see a way to help you with your problems with the car company.
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Most likely, they will try to correct the error and have the title re-issued if you signed the appropriate security documents and everything else is in order. They may even try to repo. At the very least, you would still owe the money and the could sue you. You can pay a lawyer (plus repair costs, and the balance of the loan), or just pay on the car as you agreed to do when you bought it as is. A firm response would require a review of all the documents, but it first depends on who you want to pay and how much you want to risk. You could pay significant fees to try to sue for unlawful repo, even if you have a good claim against them.