By storing 10g of fat (90 calories, 3.5%-5% of daily calories) per day you accumulate 3.5 kg of fat after an year. By eating protein that cannot be utilized by your body fully (wrong amino acid profile) you are storing extra fat and build less muscle.

Whey protein most probably would bound muscle protein synthesis by methionine available, and make substantial (I think 40%) amount of calories from leucine in it to be converted to glucose. Two 33g servings of whey protein can be converted to 1g of fat, just from leucine alone.

Whether you store fat is based on whether you eat an excess of calories. Some protein being only usable as fuel is fine, because you need fuel. If that fat isn't being immediately burned, then eat slightly less.