There are loads of examples, that's a very good one (fibre burns in calorimeters so can throw calorie counts off a lot).

Raw food delivers fewer (usable) calories than cooked food, whether it's vegetables or steak.

Highly processed foods, especially carbohydrates, deliver their calories fast, spiking blood sugar and stimulating insulin production to lay the excess energy down as fat. If you're hibernating for winter, you want the fat. But if you're running a marathon you want slow (protein and fat) and slower (complex carbohydrates) release foods.

Chill your potatoes/rice/pasta for 24 hours and it will have more complex carbohydrates than it did when freshly cooked. Reheat them and they'll have even more. Jury still out on whether this means frozen chips (fries) are a healthy food...

Even the amount you chew affects the number of calories available (analogous to the amount of pre-processing being important).

International tables of glycemic index and glycemic load values 2021: a systematic review

How reheating pasta and other carbs can make them healthier