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Those are definitely some weird glitches. Sounds like the enemies are leeching off your upgrades (not intended btw). Complete transparency: I don't plan on updating this game any time soon but if I do I will make sure to fix these issues. Thanks for the heads up!

Oh, okay. I should also mention that sometimes I don't even need to have an upgrade before, sometimes it just randomly does that (like I had a run once where the enemies' bullets were always around Charge speed despite me not having Charge in that run or previous runs).