Your math is off. You assume that the bonus is a compound bonus. In reality it is a flat bonus against the base capacity.
Your medium ship has a base capacity of 75. Lets assume you research a 20% capacity increase:
Compound: 75 * (1.2) = 90
Flat: 75 * (1 + 0.2) = 75 * 1.2 = 90
No difference here.
Then you research a second 20% capacity increase:
Compound: 75 * 1.2 * 1.2 = 108
Flat: 75 * (1 + 0.2 + 0.2) = 75 * 1.4 = 105
But here is your difference.
Hope this clarifies the issue.