If you are a student paying tuition plus a (single) student fee, or one paying tuition plus multiple fees, there is probably little difference as far as you are concerned, aside from how much it all adds up to. The difference between whether there is a single fee or multiple fees on a single item is more a matter of importance for accountants or tax consultants... or for those concerned with the administrative revenue.
If you are charged multiple fees for a single item, it is because these fees are strictly applied to specific budgets (they are reserved for specific purposes). This is of little importance for the payer, except that some of the fees might be tax deductible, while others are not.
For the payer, "fee" and "fees" would be essentially the same thing, unless the "fees" have been itemized for their tax purposes (or for curiosity/accountability as to where their money is actually going).
Of course, the other usage of "fees" would be for multiple purchases, etc. I really doubt that this is the issue with your question.