Fixing bugs ... reduces score?
What I do is try to figure out what effect the bug was having, and understand why it caused better results. Then I try to add that effect back in a 'legitimate' way.
An example is when I gained score by removing the variable-bot-width, which accounted for the extra area the bot covers in a wave if it is moving while the wave crosses. I later added in precise-intersection code, which gained me more score, despite (theoretically) doing roughly the same thing as what had cost me score previously. I chalked it down to my previous method not being accurate enough.
If this was a bug in a GF gun that helped you only against wave-surfers, I'm not particularly surprised. After all, you were using something that they weren't designed to dodge.