...card can they my credit card was taken by the hotel for any extra expenses but later found out they charged me for the stay which i did not authorize

Ring them! Tell them! Warn them that if you don't get a refund, you will take legal action. Being charged twice? Not cool!

I work at a major hotel, and if you submitted your voucher there should have been no reason for the room charge. Your credit card was supposed to be for "incidentals" ONLY.
If you can't get the matter resolved with the general mgr. of the hotel, I suggest you call those who provided you the voucher, like Choice Hotels or whoever you earned your points with for the voucher. Obviously, you must be a member. If that's the case, there shouldn't be a problem crediting the charges back to your card.

Yes, call the hotel directly. It was likely a simple mistake which will be easily resolved. If not, then call the company who you paid for the pre-paid voucher, and ask that they intervene on your behalf. If need be, then document the steps you took and dispute the charge with your credit card company. Likely disputing the charge will not be necessary. This should be fairly straightforward to correct.

I would contact the hotel and have them credit you back the charges for the stay. You may have to speak to the manager. Usually, they will rectify the situation.

If they refuse, I would file a claim with your credit card company. The credit card company will send you a form to fill out. Fill it out and send in any copies of your receipts, and a copy of the pre-paid voucher.