I've been trying to duplicate this glitch for the last hour, but I have no idea how I got it to happen.
Somehow, taking 1 out of 2 upgrade for Missile Barrage made my Clunk do less damage one game. It was on Ribbit IV. Instead of doing 14/18 each shot, the missiles did 13/14. When I bought the second half of the upgrade, it put the damage to 14/18 instead of 14/18/22.
Unfortunately, I don't remember the loadout or upgrades I had purchased that match before this happened. I'll keep toying with it when I have more time and see if I can get the glitch to happen again.