I was asked to leave half way thru the job so I was only half way done and now my customer is trying to back charge me for work that wasn't completed.
Even if you have not filed a lien, if you are within 90 days of when you left the job, you still have the right to file a lien, assuming you timely served notice to owner (if you are a subcontractor). So it is perfectly reasonable for the owner to request a lien waiver to protect against your filing a lien between now and the 90th day. Of course, you should ask for payment in exchange for the lien waiver, assuming your customer still owes you for work performed.