Just to add some more up to date info:
There are different levels of dining plan. The main one includes 1 table service and 1 counter service per person per day of your vacation. This dining plan no longer includes an appetizer, and it does not include gratuity.
Also, the dining plan has been increasing in price each year, outpacing the increase in menu item prices. Pretty much to the point where you need to plan your meals to focus on the most expensive items, to assure that you're getting any value and not losing $10-$15 a day.
Also, on this dining plan, stay away from Signature dining, which requires two table service credits, as there are no entrees that cost twice as much as a regular table service entree, making the value even worse.
And, to answer the original question, yes, sometimes there could be specific menu items that are not part of the dining plan. Some dining locations could cost only one table service credit, but have an expensive meal item that is not allowed to be your dining plan entree.