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This happens and sometimes the different is significant. Without knowing exactly where you reserved and the pricing details, we cannot tell what computation was used but it's only a result of pricing structure.
A weekly rate is almost always cheaper than 7 times the daily rate, so when exceeding 6 days, even by a few hours, you get charged as a 7 day rental which gives you a better rate.
There are also discounts for rentals longer than a certain number of days and where business rentals are more common then tourist rentals, weekend prices will be cheaper, so by renting through the whole weekend, you get a discount. Some companies have a different rate for each day and add them up, while others have a daily rate that starts depending on the day. So it may be that 6 times the Saturday rate is cheaper than 5 times the Sunday rate.
Once I complained by price went up because I returned the car early and the agent could not do anything since the computer computed the rental price on return. By bringing the car in the next day, I would have gotten a lower price.