Yes this can happen- it will be clearly stated on the menu
The servers will ask if you are on the dining plan and explain your entitlements depending on whether you have the regular DDP or the Deluxe DDP. At most restaurants nothing will be excluded (within your entitlements). In the entree section of the menu we haven't come across any exclusions. For desserts the large Kitchen Sink is not incuded at Beaches and Cream.
For example any restaurant with a Prix Fixe menus may have restrictions
There are only a few restaurants with a prix fixe menu option (e.g. Les Chefs, San Angel Inn). It can be ordered on the DDP and many will because it includes an appetizer which isn't normally an entitlement on the DDP. However, no substitutions are allowed. The prix fixe is just one choice; you can order any other entree if you prefer.
Via Napoli pizzas require 2 credits I believe
Actually VN limits the pizza option on the DDP to the individual pizza. It is only rarely (think pixie dust) that someone has posted that they were allowed to use multiple credits for a larger pizza.
Marakesh and Monsieur Paul used to have options that you had to pay cash in addition to using credits.
If you order the prix fixe at Monsieur Paul or one of the Feasts at Marrakesh there is an upcharge to cover the cost of the appetizer unlike Chefs or San Angel which do not have an upcharge.