I'm going to differ from a couple of the other answers and suggest that the most likely reason is budgetary, not bureaucratic, based on what I know about my state university in the US.
The money for your tuition, and possibly some fees, comes from Graduate College. The fees you have to pay go to the University, not the Graduate College. The Graduate College does get money from the University, but only a small amount because those in charge of the University want to allocate most of their money to other areas.
Because the Graduate College has a tight budget, they decide to cover your tuition to be competitive with other grad schools, but cut some costs by not paying all (or any) of your fees. While $300 may not seem like a lot to you, multiply this by the number of grad students the Grad College supports and compare with their small budget and it might cut their expenses by 1-2%.
Also (I think this is one thing Tom Au is getting at) it may happen that the University needs to increase fees to deal with tighter budgets, and now the Grad College is not committed to covering those increased expenses in later years.
The first approach to cutting cost is often to trim expenses by a small amount in different areas to minimize effects of shrinking budgets. Were there much more serious budget cuts, you might have to pay more in fees, or get a significantly lower stipend, or have to pay for part of your tuition.