Yeah I am in agreement, but sadly the genie is out of the bottle. With how many downloads the game received I would be hesitant to release any patch for a non-critical error since most people will not manually update.
This is definitely something for me to consider should I ever make a sequel or large scale expansion. In my mind it feels I have a few options.
1) Create flowcharts like yours to ensure every puzzle has no forked solution tree. Which is fair amount of work, but doable.
2) Design additional levels like this and have Miku explicitly mention "A bomb squad member never guesses, the correct solution will always have full context" however I doubt most people will read what she says.
3) Add checks for multiple orientations of symbols for puzzles like this, which is again a fair amount of work, but doable.