Overall, I am very satisfied with the preschool my son is attending part-time, but .... I have heard some complaints from other parents mostly about administrative issues. The worst complaint I heard was from one couple who were paying full-time fees for their son, but they were never told that they could pick him up anytime before 5:30. The poor dad was killing himself to get out of work to be there by 4 only to eventually learn that was not the case. Needless to say, they were very annoyed when this was "revealed" to them, as if they should have known all along.
While I am no expert on daycares, my observation based on my own experience and what I've heard from other parents is that most daycares and preschools run on very little money, with the exception of the really high-end expensive ones. If you work out the math, it is remarkable to me that they are able to stay in business at all. The only way they are able to that I can figure out is to pay low wages to their staff, accept donations of every kind, and stretch their staff to the max. I can definitely say that about the preschool my son attends - it seems to me that the director is pretty much a one-woman-show, handling all aspects of management and finances as well as caring for a class of toddlers all day. The example I gave in the previous paragraph I think is one of lack of adequate staffing and time, not of intentional deceit.
They also have the issue of keeping the legal ratio of staff to kids, which makes part-time students tricky. At first we were told that we'd be able to choose which days of the week my son could go, but once it was out turn on the wait list and he was able to register, they only offered Thur and Friday which wasn't ideal for our schedules.
I would not hesitate to sit down with the director of the school, or arrange for a time to meet and go over the numbers with her. It is certainly your right to know how they are calculating the fees. It really does sound as if there was a mistake. Try to keep your cool in the meantime and you will get the best results. After discussion if they are still holding to the price of the part-time being more than full-time, I'd look else where! Best of luck to you!
EDITED: I just calculated some figures based on the structure of our preschool, and I think i may know why the discrepancy. Many daycares charge for full-time based on a 10 hour day (between 7:30-5:30), and part-time is often 6 or 5 hours a day. If you calculate by hour using two 10 hours days, the schedule you want is actually more hours than 5 part-time days. So maybe they aren't trying to pull your leg!