Multiple ways to solve this issue.
1) Create an option group with the list of the extras (& their specific up charge) and apply to the the items that they usually need extras on. This will actually give them an option to pick those extras & be charged for it. This is the best way to solve it. As many people are willing to pay the extra charge, but don't see an option to select those extras.
2) After step 1 is done and it continues to be a problem, you can put a note that extras/additional items put in the special instruction field will not be honored or will be charged extra. Worst case scenario, we can totally disable the special instruction box on specific items or on all the items in the menu, this way it will remove the box for them to type extras in.