Personally, I would have paid it.... You incurred the expense... it is not the hotel's fault that your company has a certain reimbursement policy.
I assume you have the folio... and never submitted it for reimbursement? Did you not wonder why you still had it? or no charge had hit your card?
Mistakes happen... but this is a legitimate charge.
In regards to your $20 issue... I will say it... do not leave money that you do not want to be taken!