What the article calls 2012-13 expenses are not. They are taken directly from the Equity in Athletics database and are called “2011” expenses on that site. Not sure if that means 2010-11 or 2011-12. Might well be the former.
You are correct that schools often categorize items differently – which sometimes makes a big difference. There are a number of items that can be billed specifically to a sport or simply made part of the overall athletic budget.
As for NJIT, one reason their expenses are so high is that they were in a league that required separate road trips to rural Virginia, Chicago, Utah, Houston, North Dakota, California, and finally Chicago again (this time for four days). In earlier years, their expenses were even higher because they rented the Prudential Center for some games.