Thank you for the information and your question. Although an employer can generally set the rules as to the accrual and use of PTO since there is no law that requires that it be offered, what they cannot do is not pay you for a day that has been worked, whether you clock in or not. In other words, you were due your regular pay for the day that you worked despite you not meeting the weekly deadline. Because of that, there should be no reason to have used your PTO time.
You should file a complaint with your HR Department. If that doesn't give you the result you are looking for, you can file a wage claim for the one day with the Wage and Hour Division of the U.S. DOL, since Florida doesn't have an agency that enforces wage and hour laws and the law, the Fair Labor Standards Act, that I am referring to about your pay, is Federal law.
But, just to be clear, there is no statute that addresses PTO and how it can be charged, however, you were entitled to your regular pay under wage and hour laws for the day you actually worked, so you should not be charged PTO. One thing to keep in mind though for the future, your employer can suspend and/or terminate you if they choose for not complying with workplace rules on timekeeping.
Please feel free to ask for clarification if needed. If none is needed, then if you could take a moment to leave a positive rating in the box above, I will receive credit for assisting you today. Thank you.