Thanks! Wow I can't believe it's been 6+ years since I made this game. I agree the learning curve is a bit rough, that was mostly intentional though also partially an artifact of me pushing against the limits of how much code PICO-8 would allow, and thus not being able to fit more puzzles in.
It's been long enough that I'd have to go back and play through again to be sure, but I think what you're describing is expected -- a switch will only flip-flop if a single input is activated, not if both inputs are activated at the same time.