Calories in / calories out doesn't account for weight gain.

Overfeeding a total of 84,000 calories to 24 men led to a weight gain of from 4 to 13 kg.

No significant correlation between total calories and body weight or fat mass. https://www.nejm.org/doi/full/10.1056/NEJM199005243222101

Effect of adding 2000 calories of ethanol to the diet. Caloric intake went from 2500 to 4500.

Weight gain was negligible.

http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.324.9385&rep=rep1&type=pdf

Same person, but with an extra 2000 calories a day of chocolate. Substantial weight gain.