I've run into a bug where saving an augment like "+20% damage" turns into like "20% area" for the next level gained. I even saved a elemental combo augment and then the next level i had two of it to pick from. Enjoying the game and all, needs more music choices though for sure.
So all % based upgrades are multiplicative, not additive.
For example:
If you had a crit chance of 10% and got a +20% upgrade you would now have 12% (multiplicative), not 30% (additive)
I hope that makes sense. You can always check your stats on the pause menu as well if you ever want to see how the numbers get affected after an upgrade.