I don't think by "bugs" he meant speedrunning techniques that we use, or else they probably wouldn't have taken out ISG. He might have been referring to smaller stuff that's not necessarily speedrun material. Though maybe I'm wrong and they removed ISG for another reason.
"So we left them in if they didn't cause any trouble"
ISG caused ALOT of trouble, same with stealing fishing rod, as it messed up your B button.
It actually seems that they infact only removed glitches that actually helped you to skip parts of the game.
Think about it. Ground jump was removed, and it was used to skip parts of DC for example.
Superslide was used to get to shadow early.
However, they did leave ways to perform RBA, but that was probably because they wasnt aware of them.
And clipping into jabujabu is not how the story goes. So they did want to fix that probably.
So yeah, they fixed all the old ways of breaking the games, that they were aware off.
Makes sense.