Can a collection agency get a lien against my car if its not paid off? I know they will file a judgement against me, but I thought the lien could not be done if I don't own it as of yet.

First, it is unlikely that a credit card company can file a lien against real property for unsecured debt. However, if they get a judgement they can garnish your salary and attach liquid assets.

Even if they were able to file a lien it would be secondary to the lender you borrowed the car loan from.