The other day my sister had to go to the bank because someone used her debit card to buy an $80 thing in Amazon even though she only had like $18 in her account. Maybe someone got a hold of your card info. My sister had to cancel her card and get a new one.
First off, no they can't. You probably forgot that you bought something like food or small items. Look at the back of the card for a website since most prepaid cards has a website for you to check balances.
Check to see if your bank has an online banking website. You should be able to log into your account and see exactly what purchases you made. There could be some service fees also. But to answer your main question, no, a company cannot charge you after the initial swipe of your card and that particular sale. If your bank doesn't have a system where you can check your account online, you need to either call them or go to your nearest branch.