It's the infamous "Plarium percentage": 2% bonus means "2% extra on your basic value". Let me explain on one Bonnie:

A Bonnie has a basic def value of 19 (the average over all 4 categories), and let's say that all of your upgrades/items/relics/etc. give you 100% bonus, so the effective strength of your Bonnie is 38.

Now, what you'd expect from a 2% increase is 19 * (1 + 100/100) * (1 + 2/100) = 38 * 1.02 = 38.76. So, the overall bonus would be (1 + 100/100) * (1 + 2/100) = 2.04, i.e., 104%.

However, Plarium computes your overall bonus as 102% because they do this: 19 * (1 + (100+2)/100) = 19 * 2.02 = 38.38.

As you can see, in this example, the bonus is exactly 1/2 of the expected, because the double bonus of your original 100% is not applied to the new bonus of 2%. If your original bonuses (what you had before the upgrade) are bigger, the difference between expected and gain would be bigger, i.e., you'd get less than 1/2 of 2%, which is what happened in your case.