This program raises issues of federalism because it, in essence, tells states what kinds of food they can and cannot serve to their students. This is a power that is not clearly given to the national government and yet the national government is wielding it in this law.
As with many federal programs, this program does not technically consist of the national government ordering states to follow certain rules. The states are voluntarily choosing to follow those rules. In this case, the rules have to do with things like nutrition and what foods students may be served. The states have to decide whether they want to follow the federal rules or whether they want to forego the federal funding. They are not technically being forced to obey the rules, but they are being told that they will lose money if they do not.
This is where federalism comes in. The national government is arguably using its spending powers to make an end run around federalism. It is arguably meddling in an area of law that is the province of the states by using its power to tax and spend.