Yeah, I've always been pretty bad at game balance and it turns out that testing every upgrade in a vacuum led me to overlook some stuff... there's another hilarious bug called "Silver Knives" where the Silver Bullet modifier from Tactical Philosopher's Stone applies to the Sakuya throwing knives (because unlike other melee weapons they count as bullets), which lets you just melt bosses in seconds and have infinite ammo oneshots for regular enemies. I found it so amusing (and good for speedruns) I never patched it out.
During development I tested all stages in what's now Score Attack Mode, which meant starting with just Gohei and Concussive Grenades. My idea was that I'd need to make sure everything was beatable with the default loadout, but it led me to STRONGLY overestimate the difficulty in later levels when you've got access to stronger implants/weapons. I didn't really adjust anything because I figured gradually getting more powerful and just tearing through stages after struggling in the beginning of the game worked with the story being all about breaking free of the dreadful existence you were trapped in, some sort of "ludonarrative harmony"... still not 100% sure I did the right choice though...